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With multiple inboxes, when I switch from one to another the inbox view is at the top rather than where I was when I switched to the other. This is new.
One inbox is a pop inbox with many messages in it. The other is an imap inbox. If I am working at say, message 2000, in the pop inbox, then switch to the imap inbox, and later switch back to the pop inbox, the inbox view is inconsistent. If there is a new message in the pop inbox when I switch back, the view starts with the newest messages including the new message. If I switch to the imap inbox and no more messages arrive in the pop inbox while I am working the imap inbox, when I switch back to the pop inbox the view starts at the oldest message (in my case #1 of 4900 - requiring a long scroll to get to the newest messages). This behavior is new in the version I am using (24.6.0) on a Mac (10.9.3) so apparently an update changed it. I'd like to always return to the bottom (newest) message when switching to the pop inbox, so if there is a preference setting for that, please let me know, I couldn't find one. Otherwise please fix it.
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The first part of this response is regarding the volumn of emails int he Inbox folder. I'm writting about this (although it is not your query) because I would not like to think you could lose all your emails.
I would strongly recommend that you do not save all of your pop emails in the Inbox folder, as it is designed to be an Inbox for incoming mail and not a general store.
You may see a folder in the FolderPane, but in reality your emails are stored in mbox files. Emails are downloaded and stored one after the other in the order downloaded. So, at this moment, you have one single mbox text File with all of your Inbox emails written one after the other into a single document.
Recommend you create some folders and manage your emails. After sorting them out, you could compact the Inbox to remove any 'marked as deleted' emails. When you delete an email, from your point of view it goes from Inbox to Trash. In reality it is still in the Inbox, 'marked as deleted', so it is still using space. When you compact your Inbox it removes those 'marked as deleted' emails.
If any corruption occurs in that file eg; TB cannot detect the end of a 'marked as deleted' email, then it may end up deleting a load of emails.
So I would not compact (a task that should be done on a regular basis) until you have organised your emails into other folders: See info on how to maintain a healthy Thunderbird and compacting - why it is so important.
Re; List of emails - view the recent incoming mail. I would advise you have the most recent at the top, then you do not need to scroll. This option works in much better way for instantly locating new mail. Click on the 'Date' column header to reverse the order. or View > Sort by > Date and descending