Confirmed, however the issue has nothing to do with multiple instance of mIRC, it's related to the prompt of the monitor file changes option.
If the prompt is there at the time the item should be unset (for any file, not just the one with that script loaded), it won't be

Code:
alias -l iseven return $iif(2 // $1,$true,$false)
alias 1Minute.Timer.Command {
  echo -st here
  if ($iseven($asctime(n))) {
    hadd -msu45 test unset 1
  }
  elseif ($hget(test,unset)) echo -st Hash not unsetting
}
//.timer1Minute.Timer -o 0 60 1Minute.Timer.Command
Then just open any loaded script file in notepad or something, add a space and save, keep the prompt in mIRC.

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