Before version 2 of the git-annex repository, files added to the SHA backends did not have their file size tracked, while files added to the WORM backend did. The file size information is used for disk free space checking.
Files added to the SHA backends after the conversion will have their file size tracked automatically. This disk free space checking is an optional feature and since you're more likely to be using more recently added files, you're unlikely to see any bad effect if you do nothing.
That said, if you have old files added to SHA backends that lack file size tracking info, here's how you can add that info. After upgrading to repository version 2, in each repository run:
git annex migrate git commit -m 'migrated keys for v2'
The usual caveats about migrating data to a new backend
apply; you will end up with unused keys that you can later clean up with
git annex unused.