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Why are some of my mails not being stored in profile?

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I recently searched for an e-mail using Windows Search (Win 7). The search term was a four-digit number that appeared both in the subject line and the text. Windows Search couldn't find it, although mails are indexed for it to find (and it normally does find them). So, I searched the inbox in Thunderbird itself, and it found the mail. I noted the date and time, then opened the 'profile' folder (Inbox.mozmsgs), arranged the mails by date, and noticed that this particular one wasn't there (although all the others on that day were). That explained the Windows Search failure. Then, in Thunderbird, I forwarded it to myself, and did another Windows Search. This time it was found, but not in the inbox (where it was), but only in sent mails (Sent.mozmsgs) where it was too, of course). So why are some mails not getting stored in Inbox.mozmsgs?

I recently searched for an e-mail using Windows Search (Win 7). The search term was a four-digit number that appeared both in the subject line and the text. Windows Search couldn't find it, although mails are indexed for it to find (and it normally does find them). So, I searched the inbox in Thunderbird itself, and it found the mail. I noted the date and time, then opened the 'profile' folder (Inbox.mozmsgs), arranged the mails by date, and noticed that this particular one wasn't there (although all the others on that day were). That explained the Windows Search failure. Then, in Thunderbird, I forwarded it to myself, and did another Windows Search. This time it was found, but not in the inbox (where it was), but only in sent mails (Sent.mozmsgs) where it was too, of course). So why are some mails not getting stored in Inbox.mozmsgs?

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Those mozmsgs folders are digests created purely to expose email messages to Windows search. They are not the working copies of your messages. Whether or not messages are stored in there is controlled by this setting:

Tools|Options|Advanced|General→System Integration|Allow Windows search to search messages

In isolated cases, the specific .wdseml files in those folders might be useful to allow recovery of otherwise lost or deleted messages, but these records are not guaranteed to be complete. I would not, in particular, expect attachments to be retained.

You seem to expect to find these messages in either Inbox or Sent. Do you not file your messages? How large are your Inbox and Sent folders?

Many search tools seem disinclined to search for data made up of or containing numbers. A search of your whole profile using a competent search tool might reveal these messages, but I have to point out that if they are encoded in any way (e.g. mime, URL enoding, base-64, even HTML) the raw text you are looking for may not exist as an explicit string.

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If I open a .wdseml file from the .mozgsms folder, it opens the mail as sent or received, complete with attachments, always. 99% of the mails (at least) are in these folders, I was just wondering why the occasional one is not.

I do file some of my messages if they're for specific long-term purposes, but mostly they're working messages which I delete either immediately or after a year or so. Inbox for example contains about 3000.

Normally the four-digit number search finds the mail. This is the first time it hasn't and the reason is clear: no .wdseml file was created for this message. I was wondering why. But this is I suppose a Windows Search problem, not a Thunderbird problem, as I now realize.