Firstly, I would not advise editing and saving VASL using version 3.6 at this time unless there are specific 3.6 components that you want to add to the module. Once you save the module using v3.6, it will no longer be usable with Vassal 3.5.8. A version of VASL saved using Vassal 3.5.8 should run happily on both v3.5.8 and v3.6.
When you edit the module, do you get any messages like this:
but saying about ’ xxx GPID updated from y to z’? These indicate that the GamePiece Id’s in the module are incorrect and have been updated. Saving the module, then re-opening it should then allow you to refresh a save game.
See the discussion here Help! Fixing save files with bad PieceIds - #3 by Brent_Easton about how the Refresher works.
Regards.