The lms_account_id may be different if the course was moved to a new sub-account
If you filter the search by sub-account, UDOIT will look for the lms_account_id value for each course in our database and return those that match. However, the lms_account_id is updated during each UDOIT scan and not when a course is moved from one account to another in Canvas. This means that the course could be scanned in account A, then moved to account B, but the lms_account_id in our database will still be account A until the next UDOIT scan happens on that course, which would then update our database to account B.
To fix the issue, try running the UDOIT scan on the courses that are missing from your sub-account search results, then search again and they should be there.