I'm not sure what's happening to you or what you're really doing, but scon -r simply reset the active connexion to what it was at the begining of the actual called routine, so if you don't use scid -r in your script after using /scon or /scid, the active connexion is the last you've used.
Code:
alias just_to_be_clear {
  scon 2
  .timer -o 1 1 echo -s this timer is associated with the connexion 2 : $!network - $!server
  scon 1
  .timer -o 1 1 echo -s timer is associated with the connexion 1 : $!network - $!server
  echo -a this command is executed on scon 1 : $network - $server
  scid -r
  ;here the active connexion is set to what it was when you called the alias
}
I just want to say that when you were saying that the timer (used instead of the /scon -r) was set on scon 1 in your version (which ends at scon $scon(0)), it's not possible.

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