Sorry for all the info lol but I thought of something else I do, too:
I try to sync when I have changes only from one end. For example, if I've been working with hints on the website, I will sync that before I start doing anything in FTM. Same for the other way around, if I've been working in FTM, before I go do stuff on the website I will make sure i have synced and I have refreshed the website after that sync has completed.