It was defintly a pagination issue on my end. I ended up seeing the INDD's were made in groups of 7's and needing the 8th page added manually. Thus it would literally SHIFT the pagination.
Here files structure:
Cover
Table of Contents
Introduction
Information Section
Note Taking
Information Section
Note Taking
Etc......
Can i take 1- NoteTaking.INDD file and replecatite it across the book? Rather than opening each "InformationSection.INDD" and then Addin the "NoteTaking" manually?
I hope all this makes sense, "long time reader. first time posting" jitters haha
Digging deeper in the meantime. All of this came down to the auto check box being turned on while assembling my book. Since the INDDs are design in 7's and i still needed to add the 8th page follownig each INDD file. I was adding 7-pg documents, then batch loasin 8th-pg document, then reordering. ID was ofcourse doing its jobs in auto rearraging, but since the INDD were set up in a way that the elements on a page were not on masters and just as free floating, ID rearranges and would save the messed up version so I could go back to fix after words.
Once turned off I can arrange book freely without element-shift, then sync, number, preflight/fix, and export.
HUGE thank you to you both for helping in a huge pinch!