Update: We created a new ticket to address this usage problem. If interested, the ticket is here: https://github.com/galaxyproject/galaxy/issues/7431
In short, what you noticed and what I thought was going on turned out to still be an open issue. This manifests as incompatible connections when adding in a new or different “input type” if tools are already connected downstream based on a different (or absent) initial “input type”. We agree it would be much better if the “input type” was re-evaluated on the fly, during a workflow editing session (and that is what the ticket above is describing).
Removing all connections, then linking them back up (starting with the “input”) is how to get the “input type” to reset so that noodles will connect correctly between tools.
I am fairly certain that you can skip the “copy workflow” step I put in initially. Or instead, save a copy of your original workflow back first in case something else goes wrong and you need to start over but don’t want to completely start over!
Thanks again for reporting this 