Thank you so much for looking into this, especially since it appears to be an error by me rather than in the game itself or the modding API.
Your fix is included in the latest version: 0.3.2.
– JoeyDP
PS: I'm sorry for all the trouble my mod has caused :/.
FYI:
Factorio did a minor update today (to 1.1.25) and our savegame from yesterday didn't work anymore - desync everytime the second player tried to join.
Better Air Filter was already on 0.3.2
Disabling only Better Air Filter alone confirmed that it was this mod which caused the desync.
Loading and saving the game once in Singleplayer (like boskid suggested) did solve it and we could then continue playing (including this mod)