I know this is a little late in the thred but I was having troubles updating my chrome to phone app. I was messing around and I figured out how to fix it.
1. Use Root Explorer to remove the apk from /system/app and the folder for it from /data/data
2. Download Chrome to phone 2.0 from here
Multiupload.com - upload your files to multiple file hosting sites! and copy it into /system/app (you may need to restart)
3. Go to the market and download Download Chrome to phone 2.0 and it should install!
I have tried everything b4 but copying the apk into the /system/app dir and this just happened to work. I hope this works for other ppl too.
I can use the way you mentioned to remove system apps, but for me, the only way I seem to ever have any luck installing most system apps was, after removing the old apk from the /system/app/ folder, and then make sure it doesn't show up in the Manage Applications section under the 'all' tab in Settings, and then open a terminal and run the following commands:
# su
# mountsys
# cat /wherever/APK_you_want.apk > /system/app/APK_you_want.apk
# unmounsys
# sync
Then reboot phone and the APK will now be installed (some apps will work without having to reboot).
To verify where the APK installed to, you can use Absolute System, and click on the remove ( - ) apps button and it will load a list of all the installed apps, and then scroll to the app you just installed and it should list it as: /system/app/APK_you_want.apk in there.
The reason I say this, is because if you did successfully install your app as a system app, then you would not be able to then go to the Market and successfully install that app over the other one, so if it did, then it may not have installed before when you used Root Explorer to copy the file over. Root Explorer does work to delete the unwanted APK's from the system app folder though.
I only offer this as an alternate thing to try in case Root Explorer doesn't work for you to install a system app. I will also note that I've been able to sometimes install certain apps as system apps using Absolute System, but they wouldn't always install to the system/app folder, as they would sometimes just install to the data/app folder.
I recently figured out that the system folder and the data folder are on separate partitions on the internal flash memory drive space, so if you are always fighting with the problem of running out of disc space with all the apps you use, then open a terminal and do the su command, and then type df and near the top of the output will show you how many percent (if it's a decent terminal client), of those partitions are being used. I was only using like around 75% of my /system/ partition after I got rid of the You Tube, Car Home, stock launcher, and a bunch of other unwanted system APK's, and so I had a bunch of room to install Launcher Pro, and a bunch of other permanent-type APK's (ones that normally never get updated much in the Market) in there to fill up that partition to 95% full. Then after that, I had a ton of free space left of my /data partition, so I didn't have to have as many apps running off the SD card, since I'm sure the SD card has slower read times than the internal flash memory. So then the other apps that I leave on the Apps2SD are just ones I don't use much anyway. And now I am only using around 85% of the space on the /data partition now, so there is always enough to install things from the Market on-the-fly now without worry