It's been long running where we are usually missing at least one player due to scheduling, however another has begun missing sessions so we run with 4 of 6 habitually now. The campaign is a modified version of Hoard of the Dragon Queen, which is rather linear and requires the party to travel together, so they are always in close proximity and I can't come up with great excuses why missing players would not take part in combat.

I often scale combat based on the number of player characters, usually by removing minions and reducing enemy hit points, keeping the difficulty level as it should be, but I don't explicitly tell players this. The last session however became a problem because we played with 3 of 6 players (really 3 of 5 now).

In this instance, I decided to play the player characters and was frustrated with my decision. It still took nearly twice as long as it should have even though I didn't roll for the players or enemies, just described what happened. And I felt afterward like I was taking most of the narrative shaping out of the players who were actually present!

I spoke with one of the players after who used to DM, and conjectured splitting the party narratively so the missing players are doing some useful thing, such as scouting to find the missing villain, and then just balancing any encounters for less players.

I was going to develop a spreadsheet of ideas for what missing players would be doing, while the players are off doing their own thing. Does anyone have any great ideas or techniques they use for this? If a player character were to die in an encounter, I don't want them to feel like the missing player characters would have been able to prevent it.

Magical Curses work.  Oh, X has been struck by the dreaded shrunken sleep bout.  Who knows when he will wake up and return to normal size.  For now, let's put him in my pocket.

It sounds like you have it well in hand. The only other suggestion I have is maybe have a second game running that is off the cuff so, you can adapt it more easily on the fly. Perhaps some homebrew stuff you've been thinking about. You could always just take a break from a session that people are missing.

I always did chaos fog. Why is there a strange fog in the desert? What happen to Phil? Etc. Also if you need the party to level at the same time, just give out free levels.

I think a lot depends on the circumstances of your missing players.  For example, if someone tells me ahead of time that they will miss a session or sessions, I can usually find a narrative reason to have them leave the party briefly.  Recently, we had a fighter gone to visit the grave of his mentor.

If an absence is unexpected or the party is in a place where someone couldn't easily leave, I have one of the other players run that character.  AS a GM, you are busy enough running the session, that you don't need to take on extra work.  As for why the character is acting differently or contributing less, a quick in game excuse will help preserve your narrative. For example, "You notice that Jerrik seems a bit dazed. A quick medicine check tells you that his body is having trouble shaking off the effects of that fungus he inhaled.  Perhaps he is allergic to it.  The cleric is certain he will recover with time."  

I have this problem in one of my campaigns frequently.  I've found the easiest way is to ask the missing player if they mind if another player runs their character for the session or offer to do it myself as the DM (their preference).  If I end up running the character when their turn comes up I will ask the other party members how they'd like them to use their turn.  I'll also offer suggestions if they are not familiar with the character enough.  

I also allow the missing players to level at the same pace as the present ones to not create more encounter imbalance.  

For one character... I run the character as an NPC for RP purposes. In combat, I have the players decide what he will do, where he will move, etc. I do track his hp and stuff but this is trivial to do in Foundry. I also do sometimes need to remind them of his rogue abilities since none of the rest of them have played a rogue (i.e., they may forget they can sneak attack, forget they can bonus action disengage, that kind of thing). This allows me not to have to constantly shift encounter difficulties on the fly, and keeps the character with the party for when the player returns.

But if it turns into multiple players, I would not want to do that... so I guess having them be "off-screen" might be a better option. 

Alternatively, if you are down to 3 of 6 reliable players, you might want to consider putting that campaign on pause and starting another one with the reliable players. Then when everyone shows, you do Hoard, and when only those 3 show, you continue with LMOP or whatever you guys are doing as a smaller group.

Thanks for the input everyone. I am thinking I will be more aggressive about splittign the party when a player is not present. In this case, it was in a dungeon but there are always tasks an NPC can do, such as holding a rear position, guarding a makeshift camp, etc. as it has always been implied players who are not present can not have their character die, it is a bit wrongheaded to put them in combat like I have been doing.

I also bought a guide on Dungeon Master's Guild called "I had to go because..." which generates a reason for having a player not attend in a short absence. They are all story ideas which allows the player to have their own mini one shot as well, or give them backstory for when they re-enter the campaign. Not great in the middle of a dungeon, but good for players with short absences.

I try not to overthink it and just ignore it. Player not there=character not there, for good or for ill. Rogue missing, guess we won’t be picking any locks today. Next session, they re-appear. If this were a novel, you’d wonder why a character is missing and the rogue didn’t pick the lock. But this is a game and it’s easy enough to ignore.

Quote from Xalthu >>

I try not to overthink it and just ignore it. Player not there=character not there, for good or for ill. Rogue missing, guess we won’t be picking any locks today. Next session, they re-appear. If this were a novel, you’d wonder why a character is missing and the rogue didn’t pick the lock. But this is a game and it’s easy enough to ignore.

Yep. At my table even if a player hasn't shown up for months but suddenly can/does show up, it's a given that such-and-such PC "finally woke up from his drunken slumber" doesn't necessarily matter in the end of the day. It is probably more helpful than not to try to know in advance who may or may not show up for better combat/encounter balancing though as you've mentioned. If it's for reason extremely important for PC#3 to be present in-person for some sort of greater purpose or story narrative reason, just find a way to stretch out what's currently going on (expand into bigger dungeon or side quest)

Quote from Xalthu >>

I try not to overthink it and just ignore it. Player not there=character not there, for good or for ill. Rogue missing, guess we won’t be picking any locks today. Next session, they re-appear. If this were a novel, you’d wonder why a character is missing and the rogue didn’t pick the lock. But this is a game and it’s easy enough to ignore.

I would tend to agree if someone is being irresponsible and just not showing up. But I think if there is a real reason for it, such as in my group's case where our rogue is having major family health issues to deal with, I prefer to leave the character there. I know the player enjoys reading journal entries that sometime mention his character, and I have recorded our Google Meet sessions and posted them privately to YouTube for him to listen to while doing mindless tasks around the house. I don't know how much he has actually listened, but I think it will give him a kick to hear his character doing stuff. I know he was happy to hear that his character has the most kills so far in the campaign. He's doing an unusual build (str-based rogue instead of dex) and I think he is glad to hear that his build is working well, even if he can't play it himself.

I think in this and all matters you have to go with what works for the situation. For someone who has extenuating circumstances that prevent joining you, it's important not to make it feel like a punishment that his character wasn't there. On the other hand if the person is just blowing you off, well, then you blow his character off... that's fair.

I don’t think of it as blowing them off, just they aren’t there. I don’t want to make decisions for what someone else’s character would do, as a player or a DM, so we just leave them out for the session. Also, I don’t like being in a place where I’m deciding what’s “irresponsible.” Some cases certainly it’s obvious, but in others it comes down to a value judgement, and I’m not going to tell someone else what their priorities should be. So rather than get into that mess, I avoid it for everyone, all the time.
Either way, The character still gets full xp for the session. Usually the only “penalty” is not being there to advocate for themselves in terms of treasure distribution. 
It can get weird when we start a session right after a fight and most of the part is beat up, while one person is fresh as a daisy, but in this edition that sorts itself after a long rest. 

Biowizard brings up some common points.  No shows and why the are no shows. How it is handled depends on the group. My current homebrew standard is. If necessary an npc will be ran by the party with the DM overuling if necessary. No shows will be given free levels if necessary to keep up with the group.