imported comment rotated clockwise 90 degree

I can explain why this happens, but unfortunately don't have a good solution to avoid the problem:

A PDF file can have a rotation flag that indicates if Acrobat (or any well behaved PDF viewer and printer) should rotate the page before it gets displayed. Let's say you scan a few letter sized pages, but the way your scanner rotates the pages, it looks like they are all rotated by 90 degree clock-wise. You don't want to have to tilt your head every time  you want to read this document, so you rotate them in Acrobat by 90 degrees counter clock wise (ccw), and the content finally looks correct. Acrobat does not actually rotate the page contents, it just saves a rotate property for the page(s), and Acrobat knows that before the page gets displayed, it needs to be rotated 90 deg ccw. Now the problem is that when you add annotations to such a page, they will be rotated as well, so that they match the page (and look correct when you display them in Acrobat). However, if you now replace one of these pages with a page that you created e.g. in MS Word, that page is very likely not rotated, and therefore does not have the rotate property (or it is set to 0 deg), This replaces your page image, but all of a sudden, the orientation (and position) of your annotations is wrong. The same thing happens when you export the comments from one document and import into a document with a different page rotation.

If you know what the source rotation was, and what the target rotation needs to be, you can take the coordinates and rotation flags from the saved comments file, and transform them so that they match the new file, and write out a modified comments file. A few years ago, I wrote a script that did that for one specific case, but unfortunately, I don't have access to that script anymore.