Hi @meraki :
Each apps folder is a local git repository . bench update try to update each app from remote repository, so if bench update detects any change on your local folder that as not commited to remote repository, then stops and gives you 2 options:
1. Using git commands (git pull / git pull --rebase) try to merge 2 sources and fix conflicts, or git stash to temporarily move the changes …
2. bench update --reset discarding all your local changes and overwriting with remote repositories content.
I don’t know what kind of changes you did on your apps before bench update --reset but they are gone if no backup was made.
Hope this helps.