Wonderful! I nearly tore my hair out though. The short story is do not put spaces or dashes in tag names. Something with the metadata breaks the sync. AesSync will see the files modified, but fail to sync.

This did end up with me writing my first CLI batch file for Aesprite! 

It shows a selectable list of character folders, then a choice of sprite, finally converting using tags...

From:
...\Sprite_Bases\Character.aesprite

To:
...\Sprite_Sets\Character\{Sprite Name}\{Tag}.aesprite

All I do now is update a master sheet, and run my batch file!  This is great!