macOS: Sequoia (15.7.3)
BetterTouchTool: 6.108
After update to v6108 lost half of my CAGs, reverted back to v6107 and they appeared again 
there are only (mostly cosmetic) 4 lines of code changed between 6.107 and 6.108 and none of them related to CAGs. I don't think this is possible.
Do you maybe have the experimental icloud / dropbox sync active?
I'd try to delete the three 6.108 database files and try upgrading again, maybe just some hiccup during database migration:
- ~/Library/Application Support/BetterTouchTool/btt_data_store.version_6_108_build_2026012401-wal
- ~/Library/Application Support/BetterTouchTool/btt_data_store.version_6_108_build_2026012401
- ~/Library/Application Support/BetterTouchTool/btt_data_store.version_6_108_build_2026012401-shm
no not using experimental icloud/dropbox, nothing changed there. But I installed the smooth scoll preset which works nicely in 1.08 with trackpad. disabled the preset as it doesnt work with 1.07 as you know. Nothing changed between 1.07 and 08 in my setup
gives:
rolled back to 1.07 for now
Edit: Just noticed that the scroll_mouse_move preset becomes the master preset after updating to 1.08. My original master preset is not in the list of presets then. Reverting back to 1.07 gets my master preset and thus the CAGs back.
You need to delete the mentioned database files while you are on 6.107, then upgrade to 6.108 so it can redo the database migration
(alternatively export your preset in 6.107 and reimport it in 6.108)