The files in the "Shared" folder have to match the specific server version as the format changes from time to time. Just delete all the files in the "Shared" folder- they will be rebuilt by running the new version of the shared_memory.exe program.
Since you have copied the repack files into your new folder (presumably it has the quests, maps etc folders as well as your config files). You would only need to update the newly compiled exe files.
The "bin" folder I mentioned was the "bin" folder where you compiled the newest source. e.g. C:\EQ\Source\Build\Bin\Debug in step 4 e) of the windows setup guide. When you do your compile the newest version of the EqEmu server (it's actually several programs) will be put there.
You would take the newly compiled shared_memory.exe, eqlaunch.exe, queryserv.exe, ucs.exe, world.exe and zone.exe from the C:\EQ\Source\Build\Bin\Debug folder and then copy into the new server folder.
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