You have GML - so, plain text - code in your project that can be copied and pasted without any problems, and yet, rather than doing that, you did not just go for the vastly inferior option of screenshotting the code, but outright took a photo of it with a camera... that's one of the things I don't understand.
Before you do anything else, do yourself and everyone else a favor and learn how to screenshot:
By taking a screenshot, you can capture an image of your entire display—or just an area of it. Windows 10 has a variety of built-in tools for easily capturing a screenshot, and we’ve also got some even more powerful third-party tools to recommend.
www.howtogeek.com
That aside, when we ask you to "post your code with full context", that means
any and all code that is related to the issue. So if your problem has to do with deactivated instances after going to different rooms, that includes any code that handles activation
and going to different rooms. The way I see it right now is that your pause pauses absolutely everything, so it should be impossible to go to a different room while the game is paused (as you have not posted any code that is capable of going to a different room while the game is paused). That code would have to be in the only object that doesn't get deactivated during pauses. Is that the case?
I don't see any way for the code you posted to fail without external influence (e.g. changing rooms, which will leave deactivated instances behind). You said it yourself that you are doing this, but you didn't post any code that actually does that. So, like before, I have no idea
what you are actually doing that leads to this issue, because the code you posted - by itself - can not physically cause the problem you describe because it does not go to any room. Get what I mean about the "full context"?