Help, I edited a text box in a book and now the entire file format is completely off

I was fixing the margins on one of my book files, a little over 300 pages, and 23 documents (intro, chapter pages, and outro) for the document. However midway through fixing this issue some of my chapter documents, not all, now start on the left hand side instead of the right regardless of if the document before had a lefthand page or not. The second chapter (third document) now starts on the left, and the last two pages are completly out of sync, going from page 43 to page 36, dispite being selected as automatic page numbering, and though I somehow managed to fix the issue and get them correctly numbered, the numbers are now in brackets [44, 45] which none of my other page numbers are. As well, on the affected documents, any blank pages I had have just dissapeared. 

I'm almost positive it is a glitch, as some chapters load with it on the right hand, but when I switch to it later its on the left hand.

The only thing I can think of is that I synched everything style wise with the CH 1 document in the book before editing, but CH 1 starts on the right hand side, and not all pages have been affected.

I was only editing the parent pages, I never touched the interior of the documents, and it was only by 0.01" to fix a printing error for internal margins.