When reverse engineering a query in the Query Builder, parts of my query are gone, the format has (4241964)

When I reverse engineer a query of mine in the Query Builder, I run into several issue.

1) A couple of lines in the where clause are being removed.
2) The format of the query is changed, so it is not lined up and look nice, like it was previously.
3) Get a "The query cannot be modeled. You can execute the query without modeling it or correct the flagged problems to continue." error for comments that are included in the query.

WORKAROUND:
None

STATUS:
Waiting for a fix to be released in a future version of Toad for Data Analysts.