There is a simple way around: Don’t run your 50 instances from your build output directory. Copy your binaries from your build output to another directory and start your instances from there.
If you do so, you won’t have problems deploying a new modified version. Of course you cannot exchange the running binaries with that new version, but you may copy your new version to another directory and start it from there.
UPDATE: Another way around would be to temporarily change the output directory of your deploy process. But I’d prefer to move productive binaries away from the build output location.
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solved c# “Unable to copy… because being used by another process” when building