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.