Searching by check number after upgrading to 5.5.0
I was able to replicate this issue.

Historically, CiviCRM didn't support multiple payments on a single contribution.  So the check number is part of the contribution.  However, now that it supports multiple payments, the check number is part of the financial transaction.

The check number being searched is the contribution's, not the financial transaction's.  I think it needs to be changed; I can't think of a case where it's desirable not to.

I just opened a ticket on https://lab.civicrm.org, financial#37.