Working in Germany on Czech Visa

I am an Indian national working for an Indian IT company and am currently working on a project in Frankfurt, Germany. I am concerned about my visa status and I think I might end up in a really bad situation.

I have a short-term Schengen visa issued by Czech Republic. My company has a branch in Czech, which gave me the invite for this. I used that visa to enter Germany. Now, I will be in Germany for 85 days and go back to India after that. My company wants me to come back to Germany after that. For this, they have got a Czech Work Permit for me through their Czech branch. When I go back to India, they want me to immediately apply for a short-term and a long-term (yes, both) visas at the Czech embassy based on the work permit. The logic is that long-term takes 4 months and in the meantime i can get another short term visa and fly back asap.

Now this seems to be stretching it too far. Firstly, I am using Czech issued Schengen visas to enter Germany after have stayed there 85 days already. This might make the Frankfurt German immigration suspicious. And secondly, I think that the 90/180 rule will apply for this short-term visa as well, so I will not be able to enter Germany.

What are the problems which might come up? Can somebody help?

"Your" company seems to have an "interesting" view on immigration. To legally work in any EU country you would need a work permit for that country and you would have to go through the required process (short-cut via two applications, seriously?). You say, you are currently working in Germany on a short term visa while you have actually been invited by a Czech compnay. The 90/180 rule does of course apply for short-term visa. I think, you should foremost be concerned about your current situation.

Inform your company about the Van Der Elst visa.