Last session one of the characters in my group died. But he got back because someone casted Resurrection on him.
is there a way I can modify his character in Dnd Beyond so the −4 penalty is accounted on his Saving Throws, Attack rolls and ability checks?

If you click on "manage" in the corresponding section of the charsheet, and then on the value you want to modify in the popup sidebar, you'll get the option to customize it manually.

You can also create a homebrew item that gives a -4 penalty to all those things, then equip it on the character sheet. It's a little less work than editing each thing on the character sheet. Then as each day goes by you can either edit the item or swap it out for one that has a smaller penalty.

You could use feats. Make four feats called “resurrection penalty 1” through “resurrection penalty 4.” And attach them all directly to the character sheet under “Features and Traits->Feats->Manage Feats.” Every morning that the PC wakes up the Player just removes one of them (using the same area of their character sheet) until they’re all gone. Each one can be identical other than the name so it won’t even matter which order they get removed. Each one will use the same 4 modifiers:

1. Modifier: Bonus->Subtype: Ability Checks->Fixed Value;  -1
2. Modifier: Bonus->Subtype: Saving Throws->Fixed Value;  -1
3. Modifier: Bonus->Subtype: Ranged Attacks->Fixed Value;  -1
4. Modifier: Bonus->Subtype: Melee Attacks->Fixed Value;  -1

Each of those feats will then apply a -1 “bonus” to those rolls and every time they remove one the total -4 will get smaller.

Thank you, this is probably the best solution since it can be applied quickly. There are already pre made feats by other users you can use.

I may be mistaken, but I believe those were made by one of the previous people that I told how to do that. (Technically we’re not supposed to publish feats that aren’t feats like that, so I won’t tell if you don’t. But let’s just hope a Mod doesn’t see them. 🤫