1. I am on H-1B with my I-140 approved in EB-3 with priority date is Sep 2013. I have 12+ years experience in the field. I am getting an opportunity from a company. They are ready to start my green card process.
I have just completed my master degree(MCA) from India. Waiting for my degree certificate, which would take a month or two.
2. Can my new employer do the H-1B transfer now based on my BSc degree (Computer Science) and once I get the master degree certificate, can they start the green card process in EB-2? Or do I need to wait for my master degree certificate before the H-1B transfer?
See clip from Attorney Rajiv S. Khanna's conference call video that addresses this question.
That is not required. If you can get the school to give you a letter that says you have finished all your degree requirements and you are waiting for formal confirmation of diploma or degree, that's good enough. But you can't be in a situation where you have taken the examination but results has not come yet, who knows you may not be able to pass.
So, if you have completed all requirements that is research or credits, whatever it is. If you have done those and you are nearly waiting for formal certificate, that is no problem. You can go ahead as you have got your degree already.
Regarding Question 2 the answer largely depends upon the lawyers. Have them review it. There could be potential legal issue. But if your degree requirements are completed and they induct you , employer inducts you or a job requires the masters degree or equivalent, you should be able to use that degree certificate when it comes or even started now. This is an issue which needs to be discussed with your lawyers in detail.