Cosmos 2499 is in this list of amateur radio satellites and according to Gunter's space page it contains amateur radio packages, and are 'secretive', and performed proximity maneuvers with its launch stage. Why would something that sounds like a spy satellite also carry an amateur radio payload? Would that not just make it easier to track?
There is an excellent article about Cosmos 2499 that explains some of the history of the satellite. One of the things in particular is the following:
According to Ostapenko, the satellites were developed in cooperation between Roskosmos and the Russian Academy of Sciences and were used for peaceful purposes including unspecified research by educational institutions.
So some of the research was Roskosmos, some of it from scientists. Also, RS-47, the "Amateur payload", was detected quite late on in the process.
It turns out that the RS in RS-47 is "Radio Sputnik". A list of all such satellites can be found at this site. Some of these I know for a fact had no amateur radio payload.
Sample telemetry from the system is shown at this site. Note that the signal is only one-way, and morse code. It is broadcasting in the amateur band, but only seems to be a one way signal in that band.
RS47 UBS 164 UAB 163 IBS 0 IAB 126 MPWA 0 MPWB 129 VTXA 155 TTXB 153 TNAP 152 TGBV 152 TCON 157 MCON 69 SMA 72 SMB 67 MRXA 26 MRXB 14
RS47 UBS 164 UAB 163 IBS 0 IAB 126 MPWA 0 MPWB 129 TTXA 155 TTXB 153 TNAP 151 TGBV 152 TCON 157 MCON 69 SMA 72 SMB 68 MRXA 26 MRXB 14
This is coming down in morse code, on a frequency allocated to amateur radio. It seems a bit unusual how this would have gotten on a satellite as secretive as you mentioned. It could have a few purposes. First, it might be to defuse the potentially dangerous situation of a secret maneuverable satellite. It might be some kind of message passing test between satellites that for some reason was done over amateur frequencies. It might even be a student project at one of the universities only to be done after the primary mission of the satellite was complete. I can't find a specific reason for why the payload was included.