Hi Rafal,
I think, that such a smart code-generating feature cannot be created using simple GTL in xdb file. I think, that you should create an automation, which would create a model from your current DB (perhaps archive model capabilities can be used for that) BEFORE you trigger the "Apply model changes to DB". After the changes are performed in DB, you should run it again, but from the archived model into current (and already modified) DB. Then you will get your undo scripts for your exact changes using only standard functions of PD (archive model, ModifyDatabase function). Perhaps you will need to adjust this proposed process according to the capabilities of functions present in PD API.
HTH,
Ondrej