Biggsy, have you been tagging those files between syncs? Playing them, so that the play count has been updated?
If so the Date Modified of those 3,500 files had changed, and if you had the "Resync if Data Modified has changed" setting ticked, MC naturally had to resync them. Note that if you want Play Counts to be updated on your device and shared back to MC, you need to have this setting ticked. But if your device doesn't update Play Counts there isn't much point. (I haven't tested the update of Play Counts back from a device to MC, but some people say it works.)
Before a sync, when you look at the Device under "Drives & Devices", what does the Status column show? "On Device"?
Are you plugging the SD card directly into a reader on the PC? If so, does it always get the same drive letter assigned?
Sometimes Handheld Sync can get out of whack, and a "Recheck Sync" is required to get it back on track. Particularly if you have deleted or copied files outside of MC. Note that Handheld Sync can be set to delete files that are no longer in the sync list, so no need to delete the previous files first. By using Handheld Sync to do the deletion and transfer of new files, it will keep a proper record of what is on the Device, and what it needs to do with files.
See
https://yabb.jriver.com/interact/index.php/topic,114733.msg793561.html#msg793561 including the Wiki articles and search the forum for the extensive posts on Handheld Sync.