There are incompatible Java libraries between Email Template and Email Connector. When I migrate from Email Template to Email Connector I do it with two branches. The first has both modules in, and I use this to run the migration utility to get all the data across into Email Connector. The second branch is based on the first. This removes Email Template (cleaning up the userlib as this is where the conflicts are) and reworks any microflows that used it to use Email Connector. When I deploy, I do the first branch, migrate the data, then deploy the second. Once I've confirmed this is all working, the second branch is merged back into the mainline.
There may be a better way to do this, but I have found this to be reliable.