You could change the even to just include '#' for all channels, then set an exception list in the nlcheck alias.
e.g.
on *:PART:#:{
.timerpc $+ $ticks -m 1 100 nlcheck $chan
}
alias -l nlcheck {
var %nopart = #Chan1 #Chan2 #Chan3
if (!$istok(%nopart,$1,32)) && ($nick($1,0) == 1) {
part $1
}
}
%nopart are channels that it should not part from, separated by a space.