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I got hit with the painful PR0 penalty about 8 months ago. Eventually my home page was reinstated, but it looked like all internal pages still had PR0. I am getting the feeling that this is a long-term penalty, since I haven't heard too many stories about people recovering fully from it. However, it was recently pointed out to me that in fact a few of my internal pages do actually have a page rank of 1. The difference between the pages with and without this negligible PR is that the ones without are only linked to using the folder name instead of the filename. For example:
[mycompany.com...] = PR0
[mycompany.com...] = PR1
This is the case with about 20% of my files -- the URLS to home pages have PR1, the URLs to folders containing them have PR0.
So my question is: do you think it's a good idea for me to go through my site and change all the links to refer to homepage files instead of the folders that contain them?
Thanks in advance for your feedback.
But I doubt changing folder names will make any difference for you at this stage. You COULD change your domain name which would get your site totally in the clear (making sure, of course, that you don't use linkfarms/cross-linking/or anything that may of caused the trouble in the first place!)
Speaking of slight changes, I noticed that the site in your profile has a darkblue email link on a lightblue background at the bottom of your pages. It's possible that an algorithm could misconstrue that as blue text on a blue background (i.e., a hidden link). You might investigate that as a potential source of problems.