well, as i indicated: it's just a procedure that seems reasonable. i didn't test it myself.
as for partitions -- i may be mistaken, but doesn't bm just backup the files, not the partitions? if so, then you may of course get in trouble if your enlarged partition contains more data then a normal sized partition can hold, but that's the only caveat i see here.

but except for the kernel which is flashed to its own partition, everything should be available as normal files. so, just as matter of caution, you may do an rsync as root.

and rsync may well serve your purpose anyway -- after all, you get an information about differences between source and destination.
and if you flash the new n900 to vanilla state, rsync its contents to your host computer and rsync the faulty n900's contenst to your host, too (different folder, of course), you can easily diff both folders and identify any changes you made.

for the kernel, there should be the package data somewhere and you can also check with
uname -a
to see which kernel you flashed