Try going to the master page, and before you reset the margins, go to Layout>Layout Adjustment and check the Enable box. Have a good look over your document before you save, or better yet, save-as with a different name, just in case you need to go back to the original.
DON'T "reapply" the master pages if you don't have to. As long as you haven't done anything to override and alter on the document pages the frames you are editing on the masters, the pages will automatically update. If you reapply a master, any overridden frames will remain, and new copies of the master objects will also be introduced. This can cause problems of duplicate objectys showing, and in the case of master text frames it can cause trouble for text flow under some conditions.
I'm afraid I already did this and I indeed had to fix a lot of pages. It looks OK now again, though.
I think I had (still have) a mixture of overriden main text frames and not in my document. I was under the impression that overriding happens automatically because I would otherwise see any content from the masters in my document's text frames.
Do I understand it correctly and don't you have to override anything on a normal page? But isn't a flow of the story in the text objects automatically overridin/detaching them? I understand teh logic of frames on master pages appearing on the other pages (like the footer elements). But I do not quite understand I do not quite understand the logic of a 'main text flow frame' on a master and the 'text flow frames' on the normal pages..
Empty master placeholder frames are overridden automatically when you place content into them, so when you reapply the master page you get an extra invisble placeholder frame behind the overriden one. It's not necessarily a problem, but it can be if you remove the overriden frame and don't expect there to be anything there.
The only time you need to manually override a frame is if you need to edit it. You can place text or an image into a master frame without overriding first. In fact, if you are trying to flow text you should not override a master frame when using the autoflow feature. An overridden frame is no longer connected to the master frames on subsequent pages, so instead of using, and overriding those frames as text is added, ID creates a new set of frames on pages based on the margin and column guides.