Links rotate 90° when page is replaced.

This has to do with the page rotation of your two different pages (the original and the replacement page). Just because you see a page that is in portrait orientation, with lines going horizontally, does not mean that this is how the page was created. PDF has a flag that tells the rendering application how to rotate the page for display (or print). So, if your original page was created with a page rotation of 0, but you then replace it with one that has a rotation of 90 degrees applied, the links will rotate because the coordinate system changes. 

When I had this problem a some time ago and had to correct many links, I created a program to do that for me - and don’t ask, I don’t have access to that program anymore. It was for a job and remained with my then employer. 

I thought there was a preflight fix to rotate the page content and reset the page rotation flag, but I was not able to find it. It may have been in one of the other preflight tools I’ve used over the years. 

​@ControlsEng when you say pasting the links? Can you be a little more specific? Images or hyperlinks?