There seems to be a bit of confusion regarding what to do when system apps get updated while using a custom ROM. Recently Google’s Youtube app was updated with a slick new version, but many people on XDA forums & other similar communities are having issues with their rooted devices. They will get notified about an update in the market, but the installation will be unsuccessful. The same goes for the popular Adobe Flash Player. Here is a quick run down of what to do in this scenario.
It will require a third party app, typically a file explorer that can access the system partition is required. This can also be done using using the popular Titanium Backup application. Root Explorer & Estrongs File Explorer both have this capability depending on the device configuration. Estrongs takes a little extra config & may only work on CM6 variants. In settings there is an option to enable root explorer & also to mount the /system & /data directories as writable. The Root Explorer app can do this “out of the box” on a rooted device. Browse to the directory of the .apk file & enable R/W access to this path. Titanium Backup simply lets you uninstall these apps.
If you choose to use one of the file explorer methods, browse to the /system/app directory & remove the .apk you are wishing to update. In the case of Youtube, you will see a youtube.apk file. Delete this file from the directory. Reboot the device. Now head to the market to download & install the updated version. Again, the same goes for the Adobe Flash Player or any other system app you wish to update.
I hope this helps some of the confusion regarding unsuccessful updates of system apps. Now get out there & update that new Google Youtube app everyone is raving about!