I would like for it to maintain the same magnification, is this possible?
You can change the links with Adobe Acrobat (not Adobe Reader).
Thanks for takng the time to answer my question, but I must not have explained myself well enough. The links that appear on the leftside (bookmarks) are just fine, the problem is with the document size on the right.
For example, open a pdf file and set the zoom width to 125%. Then, with the bookmars open, click on a link that points to the interior portion of the document. On my screen, when doing so the document resized down to about 75% so that the entire document fits in the window, it will not stay at 125%, where I want it to remain. Can this be changed?
It's a property of the bookmark. The zoom level can either be specified, or it can be set to "Inherit Zoom", which means the current zoom settings remain the same. It seems that the creator of the file decided to specify the zoom level.
If you want to change it you can either use the free trial version of Acrobat and edit them manually one by one, or you can use this tool (created by me) which will automatically set all the bookmarks in your file(s) to "Inherit Zoom": http://try67.blogspot.com/2011/04/batch-edit-bookmarks-inherit-zoom.html
Can this be changed?
Yes with Adobe Acrobat.