So let me chime in with an alternative solution.
I'm on Win10, geany 1.36 (built on or after 2019-09-28).
Recently, I ran into this very same issue. For background info: I recently upgraded to WSL2, which required the "Virtual Machine Platform" optional feature. So, we're talking Hyper-V again, I guess. Just to be clear - I'm running a windows install, not a Geany inside the linux 'VM'.
My solution was to change the port number of the IPC socket, which is by default 49876, to another number (I randomly picked 33492). Since I was to lazy to compile, I did this by grabbing my favourite hex editor, and changing two occurences of 0xd4 0xc2 inside libgeany-0.dll to 0xd4 0x82. Now it opens files again in the same instance! Hurrah!
I believe the reason is that Hyper-V acts funny if you use ports inside the Dynamic ports range, which starts at 49152, but I didn't check that. If someone wants to publish a patch to that extend, I'm happy to experiment a bit around if another port number is wanted.
Hope this is useful for someone!

Could you give the offsets of the two 0xd4 0xc2's you changed? There are four occurrences of 0xd4 0xc2 in libgeany-0.dll.

Sure. At your own risk, obviously ;)
my libgeany-0.dll has a md5sum of 8f657bddd306134b922ba98cb4097324.
Offsets are 0x603ce and 0x603f5.
my hexdump diff looks like (original top, my changes bottom).
< 000603c0 43 6a ff d0 3d b7 00 00 00 74 27 c7 04 24 d4 c2
< 000603f0 00 00 c7 04 24 d4 c2 00 00 e8 7c 03 00 00 89 45

000603c0 43 6a ff d0 3d b7 00 00 00 74 27 c7 04 24 d4 82
000603f0 00 00 c7 04 24 d4 82 00 00 e8 7c 03 00 00 89 45


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