After installing TortoiseSVN 1.6.0, all files loaded into an AnkhSVN enabled Visual Studio 2008 project are marked as new (blue +).
I have tried re-installing AnkhSVN 2.
I noticed this too a couple of days ago. This happened because Tortoise converted your working copy to 1.6 version and Ankh doesn't know how to read it.
The solution is simple: I installed the latest daily build of Ankh (http://ankhsvn.open.collab.net/daily/) and now everything works like a charm.
Sadly this solution does not work for anyone using VS2003 since there is no daily build (SVN 1.6) for the 1.x branch of AnkhSVN.
The AnkhSVN team has stated that they are too busy right now to update AnkhSVN 1.x (ie the VS2002/VS2003 version), so it looks like unless someone is willing to help them with it (it’s open-source), there may not be an SVN1.6 version for VS2003 for a while.
I can verify that this works, too.
One thing that I ran into was that I uninstalled the older version before installing the new daily build version (I installed AnkhSvn-Daily-2.1.6649.29.msi), but once I installed the new version I didn't have any source code control integration whatsoever in Visual Studio 2008!
As it turned out, when you uninstall AnkhSVN your source code control provider gets set to "None", and you have to go to "Tools | Options | Source Control" and set it back to AnkhSVN.
Once you do that, you're good to go with Visual Studio integration and TortoiseSVN 1.6.