I originally started this post as a question but I think this might be helpful to others so I'll post it as an answer.
I am having trouble deploying a bunch of workflows, forms, views, and SMOs to an environment so I decided to remove all forms, views, SMOs, and workflows before trying again.
The main issue was that after removing all versions and instances, the delete button in the designer was missing. I could edit the workflow and close it and get the delete button back, but then the workflow would come right back.
The problem is that earlier I had removed the category (by using the SMO tester) that these workflows were in as part of trying to delete everything. That moved all the workflows into the "all" category. Once I recreated the original category and moved the workflows into it, I was able to delete them.
This has been a frustrating and time-consuming experience.