Do you have a small tree you can test with? Always test migrating a database with a test database first. If you don't have one, create one.
A migration of data from one platform to another, from one program to another, risks being corrupted. That's the reality.
I don't know how complicated (ie; media) your FTM v6 db is, but I would recommend creating a GED and uploading to Ancestry.com on-line member tree program (you can make the tree private and not indexed, this makes the tree invisible). Tweak your data in the on-line program.
When your data is tweaked and ready, fire up FTMM2 and log on to your Ancestry account. Import the tree from ACOM. It should be seamless.
If you don't want to keep the data on the ACOM on-line tree program, do not "link* the dbs. You can trash the on-line db after importing to FTMM.