With TBE disabled this is what my toy box looks like when opening it:

Enabling TBE, this is how it appears:

And filtering by "Favorites only", nothing shows up at all:

Here's my filter settings and favorites settings in TBE:

It appears to be a recent issue as I recall seeing my favorites while using TBE in past weeks/months. I don't have any lua errors specific to this issue either, so I'm not sure what's going on.
The only lua error I had at any point just before/after I took these screenshots was this:

[string "=[C]"]: ?
[string "@WQAchievements/WQAchievements.lua"]:936: in function `Reward'
[string "@WQAchievements/WQAchievements.lua"]:289: in function `CreateQuestList'
[string "@WQAchievements/WQAchievements.lua"]:454: in function `?'
[string "@ElvUI_Libraries/Core/Ace3/AceTimer-3.0-17/AceTimer-3.0.lua"]:55: in function <...UI_Libraries/Core/Ace3/AceTimer-3.0/AceTimer-3.0.lua:50>

Locals:
(*temporary) = "bad argument #1 to '?' (Usage: local info = C_QuestLog.GetQuestTagInfo(questID))"```
But I highly doubt it's related.

fixed with version 2.28.1

Thank you for reporting this. I think I forgot to initially scan for the actually account favorites. 🙈
For now you can just set your favorites again, with TBE enabled. Sorry for the circumstances.