The nandroid.md5 file contains a set of md5 codes, one for each img file in the nandroid backup. So if you wanted to do it by hand you would compute md5 codes for each img and compare them to the values in the nandroid.md5 file (which is just a text file).
However, the simplest way of checking the integrity of the nandroid is to install a little app called AFV (Android File Verifier), written by our own Scary Alien. This app let's you check the whole lot in a single operation: just long-press on the nandroid backup (which is a folder) and select "Verify Nandroid Backup" from the options. It will recalculate all of the md5s and tell you if there are any problems.
So...when wiping for a new rom,do I clear cache, format all but SD and SD ext, and wipe dalvik? Iwiped all data and factory reset last time and then had the problem with the mismatch. Titanium backup told me that my android id had changed also.
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