The topic says it all: Is there a problem in using HFSLIP (or nlite) to integrate a hotfix that supercedes a hotfix already integrated using these tools (i.e. a "hotfix update" in the windows image), or it´s best to use a "clean" windows version and start from scratch?

There are too many variables for all the hotfixes released since day 1. Lets say you have some old IE6 updates AND IE8 updates. The end result is bad. Same for mixing and matching various WMP updates. There were even some updates that where mistakes by MSFT that caused systems to continuously reboot. I'd assume you'd not want to include the "mistakes" that msft made. Whatever the case, hfslip needs to use a virgin source. I suppose if you are in a bind, you can extract each hotfix manually and replace the appropriate cabbed dlls. You'll be on your own for that though, extracting and creating your own modified installation disk is well beyond the scope of this forum.