I'm a little confused. To my knowledge if you're not using TPoint and doing "map" rather than "sync" then TheSky6 would not retain more than the last sync.
However the telescope's mount might.
For example using my LX200 I can sync all I want via TheSky6 and/or scope and the telescope and TheSky6 only know the last sync'd position. But using my GM-8 with Gemini, I can build up a model by syncing on multiple targets, but then I need to do that on the Gemini hand controller its self. Even with the Gemini I thought syncing in TheSky simply syncs on that target, nothing more, no accumulative effect.
Perhaps it's more likely the difference you've experienced in the past between syncing on one target vs multiple is just setup/alignment on the night and what particular object you syncd on last ?
If your pointing was good and is now worse I would first suspect the mount has drifted off alignment slightly or some other mechanical factor is at play, or perhaps the date/time on PC and/or telescope has drifted off.
My 2c worth of random thoughts which might not help at all, but oh well!
Roger.