hiteshergef

Looks to me as though the text frames are not on the master pages and that is why they are moving.

I am fairly sure that you cannot resolve this issue automatically, rather than with manual intervention.
The margins are there purely as ‘guides’ for manual layout and do not affect any of your layers.
If you also have Designer then you could possibly use Constraints to get some kind of automatic layout re-positioning but that would make things even more complicated (and I don’t know how well it might work as I have not tried it myself).
The best thing you can do is to set the page size and margins ‘in stone’ from the start.

From the look of what you are creating (a book?) it would have been better to have created the text frames on the master page - (I believe that is the correct way to do it)
You could then have moved them all globally just by moving them on the master page
Not sure how many pages you have done so far or how many pages you have left to do. But if you anticipate that you may have a need to manually reposition the text boxes ever again in the future you may want to consider redoing the document from the start with the "correct" use of the text boxes on the master page. PS If you save this document to an appropriate format you may be able to reimport all the text easily (in one go) into the new document.
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Runs & hides
 

Sorry to say this but as carl123 said you should make your text frames on the Master Pages, remember to link them, and then when you resize them the pages' text frames will resize automatically. And as GarryP stated the Margins are really only guides, I mostly just ignore them.

It can be hard to understand.
Sorry, but I was busy and did not have time to download your file, which you now seem to have removed. But you now know the area to look at further, and have a fix for the immediate problem

My guess: it's some combination of your widows and orphans settings, and your keep together settings.
But without having a sample .afpub document that demonstrates the problem it will probably remain a guess.

It appears to me to be your widows and orphan settings. I don't see any selected in your Styles panel.
I noticed you have only one master page for all of your content. Have you considered adding separate master pages? For example, title page, copyright, dedication, end matter?
A separate Content Master, where you would load and flow your novel's content, can be used for page numbering at the bottom of pages or the top.
If you do a google search for the words Affinity Publisher + what it is you are looking for, plenty of videos will pop up for you to peruse at your leisure. That's how I learned to use multiple Master Pages, as well as page numbering, etc.
I've been using Publisher successfully for quite a while now. As I'm becoming more familiar with the program and start to use it to it's full potential, I find Walt to be a tireless advocate and answerer of my questions. Thanks, Walt.

I have three of my e-books prepared for print books so far. Without Publisher I'd never have done it. It was quite a learning curve, but I dedicated an entire day to watching videos. (You have no idea how strongly I dislike watching instructional videos.) By the end of that day, I was completely fed up. The next day, in four hours, I had my first print book pdf-ready for printing. That included the cover I did in Aphoto. I use KDP's cover patterns depending on the number of pages in the print book. It all works like a charm.
I have used Designer to prepare two vector covers as well. Piece of cake.
The templates I have saved in Publisher have saved my bacon. Now it's merely a matter of "plugging and playing", as the old saying goes, all thanks to the beauty of the Content Master page.
Publisher also has a baseline grid manager that you might take a look at, too. I've already deleted your work, and I won't download it again to look, but it will ensure your text on facing pages lines up.