I doubt that - cfgmgr works over all devices and if it gets interrupted it will have either only worked a part of them, or none at all - never checked that. Not sure how it is programmed, but an ODM corruption I really doubt that.
pSeries and AIX Information Center
And if you are missing some new device because you pressed control-c or crashed the lpar/box, just run cfgmgr again when it's up again.
We don't take extra mksysb before running cfgmgr. You can run cfgmgr at any time afaik (but with phase 1 rules, see link above).