I've upgraded from pinstripe to rawhide 20000811. Cups was installed as the printing system, LPRng was not installed. The upgrade process overwrote files like /usr/bin/lpr from cups with files from LPRng - even without warnings in /tmp/update.log (I could have overlooked that, but I screened it for warnings, the log file is yet removed).
this is expected behaviour. /usr/bin/lpr is a binary, not a configuration file.