---Patent prosecution describes the interaction between applicants and their representatives, and a patent office with regard to a patent, or an application for a patent. Broadly, patent prosecution can be split into pre-grant prosecution, which involves negotiation with a patent office for the grant of a patent, and post-grant prosecution, which involves issues such as post-grant amendment and opposition.
Patent prosecution is distinct from patent litigation, which describes legal action relating to the infringement of patents.
From AFFY's 10K: Throughout the course of the year, Takeda has elected to limit or terminate the continued prosecution of the various U.S. and international patents covering OMONTYS, including those covering most of the European countries. We have elected, as is our right under the Agreement, not to continue prosecution of those patents when Takeda has determined to terminate its prosecution rights for such patents. Accordingly, we or Takeda will likely not be able to maintain patent protection for OMONTYS in any country, including the U.S., should the product be reintroduced into the market
to my understanding, limiting or terminating patent prosecution doesn't mean AFFY loses the patents that are already granted to them.