I have been waiting on a resolution from MS on this issue for three weeks now. They have know about it for months, but they can no longer "fix" it like they have in the past. I get an email updated every few days that says they are still looking into it. This has been happening to me for months, and in the past they would tell me to purchase it again and they would refund it. Now, they said the way it is setup they can no long do that, as a refund removes the app from your purchase history.
These are the apps (that I am aware of) I have/had this problem with:
Amazing Weather HD
WP Central
HeyDJ
Metrotube
MS (from what has been told to me) has no idea why some apps fall off our purchase history. If you login to your Microsoft Commerce account you can see that you have purchased them, but they disappear from you phones purchase history.
I have apps that I can't update as I would be charged again. Some of these I have paid for 3-4 times over again, but have been reimbursed by MS.