Sync issues - reorganizing lots of files on one Mac causes duplicates and different folder structure on second mac

I sync my files on 2 macs. Multiple times when I try to reorganize the files on one mac, using finder, it causes issues during sync with the other mac.  Some folders that were moved get moved but also have a duplicate stay in the same spot, some get moved completely, some folders are duplicated but have the files in them divided up to the old and new locations.

This happened about a month ago and I ended up turning off sync on my laptop.  Now I've turned it back on and it says it has 16,000 files to sync and will take 20+ hours.  I try leaving my computer on overnight to sync, using Amphetamine to make sure the computer stays on, but it shows the same number and time come morning.

How do I fix this without losing files? How do I prevent it from happening next time?