The issue has been fixed, but you might still have to do a one-time re-installation of mods if you haven’t played since before the issue began.
Before you start the game, I recommend that you backup your
mod-status.json file by copying it and pasting it to another location (such as your Desktop).
This file usually can be located at
C:UsersYOUR_WINDOWS_USERNAMEGamesAge of Empires 2 DEYOUR_STEAM_IDmodsmod-status.json.
Then, if you launch the game and see that your mods are missing, you can close the game, paste the file back to the original location, and launch the game again.
Hopefully then the game updates to reflect that file.
And in any case you have the complete list of your mods, their location in your mod list, and whether they’re activated.
Just make sure you backup that file before you launch the game, as it may be overwritten (due to the bug) when you next launch the game.