Compiling a program while it is running

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I have a broad question:

Suppose that I have a C++ program and I started to run it on a file in the background with some configuration which can be set internally. While it was running, I changed these internal configurations, compiled it and started to run it on another file.

Is this going to affect the previous instance which was already running in the background ? or since it was already up and running it won't ? Any ideas on this is appreciated.

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