Do you know what version you updated from and to?
Something similar happened to me, but I was able to install an older version of Manager and restore my business file from a backup which put me back into the position before all the changes to the Bank Reference field. I had to input a week or two of data again, but that was preferable to losing the cheque numbers.
I waited a few days or so, and then was able to update to the new version and in this case all my cheque numbers were preserved in the Bank reference field
This thread has the story in more detail Add custom Bank Reference field to Bank reconciluation screen