No it doesn't clear out all the codes in the remote. Instead it copies saved information from an archive area of memory to the standard location where setup codes, keymove, and macros are stored. As a user, you can't do anything that erases the IR codes.

Evidently the archive area had garbage in it.

There are two levels of reset for these remotes. The more benign is 980, and 981 will take the remote to exactly as it came from the factory, including the default setup codes.

1) Press Setup until 2 blinks
2) Enter 981
The remote should blink 4 times.

1) Press Setup until 2 blinks
2) Enter 982
The remote should blink 4 times. If it blinks twice, repeat 1 and 2 and it should now blink 4 times. This unlocks the setup code for the Cable device.

Assign setup code 01877 (00877) to the Cable device. Now the remote should control the SA box.