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.