I asked the folks who created emCore for getting Rockbox onto iPod Classics, below is a copy of the email string:
upgrade would affect whether or not emCore could be installed?
No warranty on anything, but I don't see a reason why it shouldn't work.
emCORE and Rockbox don't rely on any special data on the HDD (unlike the
apple firmware, which relies on a firmware partition being present). You
will of course have to install Rockbox again after that (i.e. unpack the
.rockbox directory, or copy it over from the old HDD).
Both also support LBA48, which is neccessary for 160GB anyway, so they
should work with drives up to 16 TB (MBR partitioning limit).