Ya, I'm going through this process right now myself. I have a Sample Flex Viewer that I've made a lot of customizations to, but as the Scalebar object is incorrect in ArcGIS Flex API 1.3 for Web Mercator, I have to upgrade to the newest APIs/SDKs for ArcGIS, Flex, and everything else.
I've been working on this since yesterday and am into the swing of things now. To start with, remove every single swc (and reference to one) from your project, and then bring in the latest ArcGIS Flex API swc (2.0). Any swc files compiled with the 1.3 version need to be recompiled (ex. Metacarta widget, GeoRSS widget, etc. - anything in the esa folder). As we're not given the source code for that, at the moment, I'm assuming all of these widgets are lost (I didn't use them/customize them, so it's not a big loss).
With just the 2.0 swc in place, go through all the problems and fix them one by one. Lots of stuff is in new locations (ex. com.esri.ags.Tasks.Query is now in com.esri.ags.Tasks.supportClasses.Query) so a lot of import statements need to be updated. Also, some objects now take new parameters/return different results. A lot of the geoprocessing tasks needed an array of graphics, but they now need an array of geometries. Other ones require new settings (ex. QueryTask.useAMF) otherwise they won't work. Just step through everything, have the Flex 2.0 API reference open, and update as necessary.
The last bit, which I'm on at the moment, has CSS declarations requiring namespaces now. Now biggie, just add @namespace mx "library://ns.adobe.com/flex/mx"; to the top of the css file, and change the declarations to mx|<component> (ex. Alert becomes mx|Alert).
There are two CSS declarations that are giving me a problem at the moment: Navigation and NavigationSlider. Obviously they're not in library://ns.adobe.com/flex/mx, so what're their namespace?
Still digging but I'll post when I find an answer...
