Just wanted to leave the solution we ended up using in case anyone else having this problem and wants to do something similar.
Rather than do a direct sync, we setup a scheduled task that saves the sql file. We created an internal webpage that reads the sql file into coldfusion (We are using coldfusion for this, but I’m sure this can be made to work lots of ways). We parse out the file removing the `feild_no_update`=’value’. The inserts are trickier, but similar thing. After that, you just schedule to execute the modified query and it works great.
Being able to sync only part of a database would be a really nice feature to have. Till something like that is added this worked for us.