Sync delete problems

Running BTT on two computers, both with everything up to date (BTT versions, OS, etc). Yesterday I created 53 new BTT shortcuts on my desktop computer. I know the number because this morning when I started my travel computer, I was greeted by a message saying, "You have deleted 53 shortcuts"! Instead of syncing them, which I have set up via Dropbox. I know how to get them back, but I wonder how to keep the problem from happening again?