Prevent Unity Editor Inspector Checkbox from having any action in-game

To sum this up the best I can: I have some code that sets a boolean value to true. When this little checkbox is enabled, it works as intended, allowing the game to function normally.

However, later on the code at some point sets this boolean to false (remember, it is a public boolean). Unfortunately, when this checkbox enabled. The console reads "true, false, true, false" etc. which prevents the desired outcome.

If I disable this checkbox, then the output reads "false, true, false, true" etc. which prevents anything from working.

Is there a way of disabling this stupid checkbox from having any effect in the game? I have tried [system.nonserialized] to no effect. At least, is there a way to disable and enable this checkbox in code?

Thanks! I hope this was clear enough.