If your version of Poser 12 is less the 12.0.1029 then it is probably saying that there is a newer version that you can download.  Not sure what you may have put in the Programs folder, however if you are worried about the Poser 12 content folder that should not be a problem.  I have downloaded and installed Poser almost 100 times and never had it mess with content in the Poser 12 Content folder.  But if you are worried about it you can (with Poser closed) rename the Poser 12 Content folder with a different name (I just put a X or the version # in front) and then download and install the newer version.  After that just rename the new Poser 12 Content folder something else and return the name to the original folder and everything should be good. 

Poser 5, 6, 7, 8, Poser Pro 9 (2012), 10 (2014), 11, 12, 13