Mobile workflow projects work properly after migration without special handling, unless you upgrade to the new workflow client containers.
Customizations made in earlier versions of several .js files in the mobile workflow package are backed up (to a .backup extension) the first time the mobile workflow package is generated in 2.1 ESD #3. They are then replaced with the new 2.1 ESD #3 version. You must manually reapply any changes you made in the earlier version.