Recommendations from Alteryx and it worked.
There is a known issue that causes this behavior when upgrading from a 10 version to an 11 version. Although there is not a patch, the good news is that there is a way to edit the workflows so that the behavior no longer occurs. A semi-colon needs to be added to the end of your connection string so that Alteryx can distinguish between the connection string and the query. This needs to be done on the old versions of the workflows, prior to being saved in 11.5. If you have saved the workflow in 11.5 and no longer have an older version of the workflow available, you can either delete the input tool and re-create the connection from scratch, or attempt to recover an auto-saved version.
Here are your options for editing your old workflows:
If you happen to still have a 10 version, you can open your workflows in the older version and add a semi-colon to the end of the connection string.
If you don't have the older version still available, and if you are comfortable editing the file manually, you can open up the file with a text editor, and add a semi-colon just before the pipe, or change it to three pipes.
connection string | query becomes connection string ;| query or connection string ||| query
