Something funky is going on with the Hit Dice. 90% of the time, they don't work the way they should and reset entirely on a long rest (instead of recovering half of them, as per the PHB Rule). AFAIK, it used to work ok.

Player's Handbook (Chapter 8 > Long Rest) : "At the end of a long rest, a character regains all lost hit points. The character also regains spent Hit Dice, up to a number of dice equal to half of the character's total number of them (minimum of one die). For example, if a character has eight Hit Dice, he or she can regain four spent Hit Dice upon finishing a long rest.

I've tried it with several characters, and the problem is recurrent.  

As always, please post links to your affected character sheets so someone can look into it for you.

Looking at my various characters again, I figured out the problem. You absolutely have to click the "take short rest" button (and "confirm") for the boxes to remain checked. Otherwise, if you check them, then leave the short rest section to manually restore your hit points, take a long rest, or do other stuff, the boxes you checked without hitting that short rest button don't register. 

In our game, we have a 10-minutes Breather rule that allows a character to spend a Hit Die (without taking a full short rest). So every time we used that rule, the checked Hit Die (Dice) never registered. Now we know!

But... aren't there places in the current rules where you can spend Hit Dice outside short rests? For example, Create Homunculus spell... It means a character spending Hit Dice after a long rest to increase the creature's hit points maximum would need to press and confirm the Take short rest button after selecting the number of hit dice. 

So... problem kinda resolved, but might encounter the issue again with features that allow spending Hit Dice outside a short rest.

Yes, there are, like, two or three other edge cases like that. The Aberrant Dragonmark feat from Eberron Rising, the Dwarven Fortitude feat from Xanathar’s, and I think there’s a Subclass somewhere too. Not a lot of them though.

I believe Hit Dice management should be moved to the HP Management section. More intuitive to look for it there, since it's also where we manually adjust the hp for them. Hit Dice boxes could be buttons that auto-rolls with digital dice when clicked (or simply checks off if not using digital dice). This way, they wouldn't be linked directly to the short rest button.