A TDM upgrade may always include a new repository version of the underlying PowerCenter installation.
Also (as of my not too recent personal experience) TDM has not been the most stable product in the world.
So for the sake of "safety" I would simply recreate all workflows. Honestly. All of them. No joke.
Yes, ugly, but it's a one-time effort during the upgrade process, so I would simply do it this way and be done. Not nice, but everything else may get you into serious trouble. I did have my share of fun with TDM, so I may look like overcautious, but I prefer to be overcautious than to experience unpleasant surprises of all kinds.
We nearly have 250+ plans and few plans have multiple workflows, regenerating workflows for all these plans manually is a tedious task.
I was planning to get it automated via shell script and when I tried regenerating workflows parallelly for two plans that are part of same project via command line it failed. Same went through when executed one after another.
Unfortunately, I didn't save the logs and they are overwritten now. Is this a known behavior?
Thanks and Regards
To be honest it's too long ago for me to judge whether this is "expected" behaviour.
For the sake of safety I would create the workflows one after the other, even though they are not related by any means. As mentioned, in earlier times TDM used to be not the most stable software, and I honestly don't know whether this has improved over the past five years.