There should be some mechanism to rebuild a folder index from ARexx, eg. a command like RESCAN from the folder menu.
(See also this post on the user mailing list:
http://www.freelists.org/post/simplemail-usr/spamfiltering-and-missing-ARexx-commands-was-Re-ARexx-and-first-impressions )
Also, the command MAILLISTTHAW should ensure to update the folder index as well.
See bug #2844656
http://sourceforge.net/tracker/?func=detail&aid=2844656&group_id=15322&atid=115322
AmigaPhil
Here is a suggested new command
(Inspired by YAM equivalent MAILUPDATE)
MAILUPDATE
----------
NAME
MailUpdate -- Update the index of the specified folder or
the current folder.
TEMPLATE
FOLDER
FUNCTION
Updates the index of the specified folder or current folder.
INPUTS
FOLDER - Name of the folder to update
RETURNS
AmigaPhil