Steps to reproduce:

Drag & drop 1 *.mp3 track into the left panel of Picard.
Have a look at the tags
Press Scan-Button
Have a look at the tags

Now write some scripting lines like

$delete(totaltracks)
$delete(discnumber)
$delete(tracknumber)

Press "Make it so"

Move the track from the right panel back to the left and press the Scan-Button again.

No change in the tags, right?

You can also delete this track and drag & drop it again.

No change in the tags, right?

Now restart Picard and drag & drop the track again.

You should now see the above 3 tag values in red.
If you press Scan, the values gets striked through on the right side of the panel.

Summary:

Changes in scripting doesn't get active immediately, at least not for the $delete - command.