I have worked for a big company in the past and I have been trying to get my 401k money but the company kept telling me that I have no money in that account. The thing is I never took it out. This has been 9 years now and now just received a letter from the company saying that I had a check for me from my 401k and it wasn't sent out. They want to re-issue out the same check to me...
My question is do I take JUST that money that was issued to me from 9 years ago or do I seek council about my interest on the money that was still with this company?

You should have been getting regular statements. If you haven't before accepting a check, you should demand an copy of the all the statements or an accounting.