[ENH] Reject version files without paths. (#5267)

## Description of changes

We're seeing version files without paths.  Refuse to create such files
and log why.  This happens rarely and should arguably fail the operation
rather than silently drop paths.

Part of this change moves the modification logic to before the
verification logic.
No sense verifying something only to immediately break it.

## Test plan

CI

## Migration plan

N/A

## Observability plan

N/A

## Documentation Changes

N/A