That‘s strange. I have to verify this with SU 12 again, but anything that is NOT under control by Sly Dolly (press key V in Sky Dolly to open the „simulation variables“ dialog - that should give you a feeling of what is supported/recorded and what not) you SHOULD be able to change during replay.
In fact, even - to some extend - what IS under control by Sky Dolly, e.g. flaps and gears: Sky Dolly will only control / change them once the recorded value actually changes. Sky Dolly will then simply (re-)set the value once the next „value change“ occurs (of the „simulation variable group“, that is).
(Sky Dolly applies a clever recording/replay algorithm that not only makes it possible to skip backwards and forwards and start/pause replay anytime you wish, WITHOUT first having to reload the entire flight - but this „on value change“ strategy also hugely saves on disk storage, RAM (once the flight is loaded) and valuable CPU cycles).
But Sky Dolly does „freeze“ the „physics calculations“ (during replay only), specifically those which would affect the aircraft position and attitude (otherwise the flight physics would constantly „fight“ the replay position - every replay tool does that). Again, you should be able to control levers and knobs (as described above) - but perhaps your aircraft also (wrongly?) „freezes“ custom simulation logic, such as „open door“ and / or „remove chocks“?