True, I am also facing the same situation. MN should have capabilities to merge PDFs, but it dosen’t have so I use another app for it. But there is no need to export pdf from MN.
Currently I manage as follow in such cases.
Merge the New pdf file(recently generated or downloaded one) into the Original pdf file of MN. (As I use icloud, I can access MN Pdfs from backdoor.)
In MN, this will create error of missing file because MN will recognise that something is missing/not right. But now, you can relink your MNNote to the newly merged file, and everything will be good again.
First Rule to follow, always add new pdf file at the end.
Second - always flattened pdf file, to get your annotations visible in MN.
With this, currently My one single MN note book have 15,000+ Notes, with 65+ pdfs attached to it. Interestingly some 15+ Pdf files have 5000-7000+ pages(& still growing) in it.
You can try this!
And, If anyone have better solution, let me know too!