No AD users:

If there are no AD accounts associated, you can have the utility locate users based on the repository username:

The SAM-Account-Name is the part of the windows login name that occurs after the \ when logging in as domain\username. This screenshot shows UPN and samAccountName:

Multiple AD users:

The utility will convert only the last user in the list of associated accounts, and remove all linked users. You can see this in the logs,

Example:

However, the utility allows you to keep the existing users, which means you can re-link the other users and re-run the utility.

While this may be tedious, you can user the user list export/import option to quickly repopulate the linked accounts. 

So, definitely make backups, especially exporting the user list and backing up the database itself in case you need to do a larger revert.

Then, run the utility multiple times. There isn't a single right way to accomplish this, but here's one possibility:

1. First run, you could convert all users that have one or more linked accounts
2. Second (and potentially more, depending on how many accounts are linked), use your backups to relink additional accounts.
   1. You can make a copy of the list and modify the copy, deleting the repo users that have been fully converted (no more linked accounts), and delete the last linked user for those that need to be re-run to convert additional users
3. Third run, to  choose the option that finds AD users based on repository username
   1. If the usernames don't match any attribute, you can change usernames as describe in this article: https://www.laserfiche.com/solutionexchange/laserfiche-account-conversion-utility/

You can make judicious use of the settings for post-conversion actions to reduce cleanup as you go, but remember that a user is considered "processed" even if only one of the AD accounts was converted and the others simply removed.