Master pages and page numbers

Two more items to note:

If you decide to go the route of creating a book and adding all of the files to that book as per Willy – which is a good recommendation – there are two ways to synchronize the book. Both are in the book panel window: Synchronize Book and Synchronize Options. Synchronize Book will copy all of the formatting from one book file to all of the others, but Synchronize Options puts you in charge. If you only want to standardize the parent pages (this is where we define our running heads), you can uncheck everything but Parent Pages to leave everything else alone. 
https://helpx.adobe.com/indesign/using/creating-book-files.html

I'm guessing you are new to InDesign books, so my other recommendation is to make a copy of the project folder so that as you're figuring this out, if you end up overriding other formatting commands by accident, you can still go back to the earlier version, figure out what went wrong and then try it again.

~Barb

To add to @Willi Adelberger answer - when you modify MasterSpread in one of the documents - you can use Synchronise option to update it in all other documents in the same Book.

You can also synchronise Char / ParaStyles, etc. 

You should synchronize your master/parent in InDesign before exporting to PDF.

Instead of merging PDFs in Acrobat Pro you can make an INDB file and include all INDD files and export from the INDB panel a single PDF. It makes combining and synchronizing much easier and results in a PDF with smaller file size.