I generally don't make changes to the ILM. I would make changes to the block and then generate a new ILM. Anyways lets assume that ultimately the ILM gets changed somehow.
Starting the flow all over again ? - This depends upon how big of the change you are making. If you are making drastic changes, then its good to start all over. But for small changes, just link the new ILM and an incremental optimization will be sufficient.
One more thing to keep in mind is that it is much easier to integrate a new ILM at the pre-route stage. Once you get into routed stage, any port changes will lead to DRCs (which of course can be fixed, but is an extra step)
ICC will think differntly with the new ILM, right? - Correct. Yes, it has to think differently otherwise it will be a dumb/useless tool.