If I alter a note, undo my changes, then set the "updated" date back to what it was before my changes, will this cause a problem with sync? Or does Joplin track other factors to know what to sync and what is done?
The fields user_updated_time and user_created_time can be changed without problems via the api, as these are only for displaying a date in the GUI, but are not used for the sync. The same applies when you change the fields in the GUI. Only are the fields updated_time and created_time in der api are for the sync process and should not simply be changed.