Incorrect 1099 from Medicare

[BHoffman]

My client provides hospice care and bills Medicare.  Medicare pays electronically and I have a report from them that shows payments made per day.  I've accounted for deposits in transit.  After comparing their report detail to the bank statement deposits, the 1099 shows as overstated by about $40k.  Pretty sure getting Medicare (National Government Services - NGS) to issue a corrected 1099 will be impossible.  

The client is a partnership. I would like the client to send a notice to NGS with supporting documents showing the correct amount along with a request for a corrected 1099, and then report the correct income on their cash basis tax return.  Does this sound feasible?  I'm not even sure IRS sends CP2000 notices to partnerships if the reported income is less than total 1099s.  I've never seen one.