Sigil supports the execution of python scripts via batch files or shell scripts. For more information see
this thread. However, you'd probably have to modify the Python script for it. (I haven't figured out the details of this feature, but
DiapDealer, who discovered it, can probably help you with this.)
If the app that generates styles with cm values instead of em values creates only a limited number of predictable cm values, you could also create a
Saved Search group in Sigil and have it replace these values automatically via a group search.