Can't get accurate count of messages in Mail

I am trying to write a script that checks the number of message in a specific mailbox in Mail. It works swimmingly, except that when I move messages out of the 'watched' folder, the count continues to include these messages that are no longer in the mailbox. Worse still, if I move a message in and out, each time I move it in, another 'phantom' message is created that will be counted on the next script run.
I have tried a repeating loop to count every message of the mailbox, and have tried flagging and unflagging, as well as moving a message in and out of the mailbox in the script, etc. to clear Mail's cache of these phantom messages, to no avail. Curiously, if I manually move a message into the mailbox from another mailbox just before running the script, the count is corrected. If the script performs this same action, however, the count is incorrect.
The only cure seems to be either quitting Mail and re-launching it before counting (not a viable option, as this script runs periodically), or deleting all messages when they leave this folder (and emptying the trash!).
Any advice? Is this just a Mail bug that I will have to live with?
Let me know if it would help for me to post my code.
Thanks!

aprilsteele,
You can add a two page pdf. Just right click on the pdf. aka (ctrl) click on it. What that does is open up a menu of options. First if it just displays an icon (ctrl) click and select (View in Place) and after you can see it (ctrl) click the pdf and select (Single Page Continuous) that way you will see both Pages or all pages in a single column.
As for the web link once the PDF is downloaded to a computer those links will become active again. Although if you actually type in a web link in the email not in the PDF attached it will act the way you want. Might I recommend adding a signature with your name, email, and website that way it will be at the bottom of every email you send.
Hope that helps.

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