I don't understand the question. When I typed cgminer -V like you asked, it returns cgminer version 3.12.0
Type in "which cgminer" without the quotes it should return /usr/bin/cgminer
It does.
No idea, I'd repeat the process.
I already tried it about four times. I even restored the firmware a couple times, just to be sure.
Edit: I was able to get it updated to 4.2.0 by using the other version instead.
The last command, that you do after cgminer has been removed or deleted,
ln -s cgminer-ants1-4.2.2a-7b8fb34 cgminer
replaces cgminer with a link to the new binary.
Thus the command
cgminer -V
would be running that new binary unless something was changed after you did the link or your path has been modified.
Somewhere in what you are doing, you have been doing something extra to undo the change.
Of course uploading the firmware will undo the change.