Each content page is linked to a specific master page and keeps the sequence. Seite1 - Page 1... Seite2-Page2. Don't jump in Master Pages because that often causes empty pages and can cause trouble. I am assuming that the sequence of your pages and master pages are sequential. I cannot upload PDF or XDP here.
The content I faked with a subform and a text field which I gave a binding repeat subform for each data item minimum 70 so that I get 2-3 sheets per Seite simulating the normal grow of content.
Each page contains dynamic content and spreads over several sheets. Depending on which Masterpage they are assigned to the numbering is done correctly. I assigned each Seite(x) with a masterpage in sequence over 2 sets.
For those to be excluded I turn off the page numbering
And it works for master pages in BOTH sets. I cannot send the sample PDF here but the Page # of ## shows only the page numbers and total for the master pages included in numbering.
The document has 24 pages but it shows only 12 in the numbering: