i would suggest doing them one at a time, especially if you have any tails - checkpoints are in a different place and in a different format, and specifying the rising column in the query is different as well. We went through this earlier in the year with around 150 inputs and did them manually.
If they're all snapshot/batch jobs, you could try to script something yourself to create the new format but it may be worth just powering through manually.
We also ingested all of the migrated inputs in our test index initially before actually replacing the v1 version with the v3 version just to be sure the data looked ok.
You may be able to migrate from v1 to v2 and then from v2 to v3, but that seemed a little too adventurous for us...and i'm relatively distrusting of automatic migrations in general, so definitely didn't want to trust 2 of them working correctly.
A couple other things we noticed....if a query has duplicate column names, it may fail in v3. Also, if doing live queries (not inputs), timestamps will be converted to strings when the results are returned - in v1, they were returned as epoch.