That is not my suggestion. You would know your case and current situations better than anyone. I am merely providing what I know so that you can make informed decision. Since you are the one who is going to be affected, all the risks and merits is up to you to decide.
Your HR seems very lenient. You clearly mentioned that they are willing to apply for new role that requires master degree, than why settle for EB3. These priority dates may move back and then you would be waiting. The only think I know is that you cannot apply under EB2 for the position your are currently working even though you have master. As long as the master was done (as someone above suggested) prior to filing the PERM and the job listing requires master, you can qualify for EB2. Again green card is for future employment. SO you could be basically working in your current position but once you have green card you could be working completely in different roles and hence HR can sponsorship for that new role. Just make sure that this new role is substantially different (according to websites it has to be 51% or more). The burden on proving it is different is on beneficiary.
Hope this helps.