D'oh! I think I tracked it down, was late when I wrote that.

/filter requires us to use the -c switch to clear the file before rewriting it. Also, I left a @Temp in there, where it should be the filename again (was originally going to do it differently.)

So, end result, change the one line:
filter -ffx $+(decks\,$nick,.txt) @Temp $+(*,$2-,*)

to this:
filter -ffxc $+(decks\,$nick,.txt) $+(decks\,$nick,.txt) $+(*,$2-,*)

Also I assume here that you're using the latest version of mIRC. If it still doesn't work let me know exactly which parts are failing. E.G.: here the remote seemed to be working but the entry wasn't being removed from the file.