My wife's Transformer Infinity exhibited basically the same behaviour after its last 2 updates (both 4.2.something, IIRC). Fortunately the backup copy of su was intact, as it likely is in your case, and I was able to restore it manually using a terminal emulater app... adb would presumably have worked as well, but my notebook wasn't available at the time. Here's what I did.
- Launch the terminal emulater of your choice (I used Better Terminal Emulater Pro, but the specific app probably doesn't matter)
- Go to the location of the backup copy.
cd /system/usr/we-need-root
- Use the su backup to obtain a root shell. This should trigger the usual superuser popup/notification, assuming that it's configured to do so.
./su-backup -
- Remount the /system partition in read/write mode.
mount -o remount,rw /system
- Copy the su backup to the proper location, taking care to keep the permissions intact.
cp -p su-backup /system/xbin/su
- Remount the /system partition in the normal, read-only mode.
mount -o remount,ro /system
- Reboot the device (might not be strictly required), to ensure that any root-enabled background apps are able to startup cleanly.
The usual disclaimers apply, of course. Your device might not have the same configuration as mine, etc., so these commands may need some tweaking. Also, if it was a 4.3 upgrade which caused you to lose root then this procedure likely won't work... I believe that su needs to be running in daemon mode in order to grant privileges, which certainly won't be the case for the backup copy (even if it is a 4.3-compatible version).