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!

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