Let me see if I understand correctly....
Are you saying you're in shapechanged/polymorphed form and you hit rest but cancel that rest (or you rest before the rest timer has elapsed) and then finding out it messes with your shapechanged/polymorphed bonuses and things?
It happens when I try to rest before the rest timer has elapsed(rest timer hits zero) while I am still in shapechanged form. The rest becomes automatically canceled and the text window tells me there is X minutes until I can rest.
The shapechange form's stats remain the same, the bonuses/stats you get from the form itself. But the rings etc that have been added in the layo merge do not give their bonuses. Default merge seem to be working, as in shield/armor/helm(not fully tested).
Example:
I have diamond wisdom jewelry, gives total +6 wisdom. Base wisdom in shapechanged form is 20. I change into bear form. I now have 26 in wisdom. I hit rest button, but I need to wait 4 more minutes until I can rest. Wisdom is now 20 and I am still in bear form.
OK thanks for the description and thanks for warning people about this issue.
Some of what happens upon resting is Bioware's fault and some is under our control, so off the top of my head, I don't know how difficult it would be to fix this for the scenario you describe. Though we interfere with the resting process, it may be that Bioware strips certain things immediately before our custom rest handler kicks in.
In the absence of any solution in code, my best suggestion is to keep a general track of your rest interval and avoid resting before it exprires. Since I know accidents happen, my more practical suggestion is to re-map/un-map the Rest function away from the "R" key and only use the Rest button under your character portrait.