Mail suddenly started retrieving e-mails starting from 1st e-mail on Server

L.S.,
I'm using the mail.app version 4.2 with POP and have been downloading my mails without problems.
I do keep the mail on the server and was at about 8000 mails on the server.
Suddenly when trying to download, the mails started downloading from the first mail.
I've stopped the downloading and am having issues, as I'm using a web-interface to read the mails and responding in mail.
I deleted the extra mails that were downloaded and from the mailbox which were the last ones to be downloaded and are duplicates and then die a Rebuild.
This took care of removing the duplicate mails and also re-indexing my mailbox.
However when trying to download again it keeps on starting from the first e-mail.
Is there a way to get it start from where the latest not download e-mails start?
Thnxs for your help.
Alecio

I went back to the vendor of the mailserver software to check your suggestion.
Their answer was as follows:
+There is no POP information stored on the server in regards to what e-mails have been downloaded or not, this is handled by the e-mail client. The client stores this information and could have become corrupt.+
Possible reasons for this to happens according to the vendor's support were:
+Have you made any changes to your connection within Apple Mail ?+
I don't recall making changes to the connection with my Apple Mail.
While abroad I recall that using one of the hotels providers, I was unable to send mail but that has to do with SMTP and shouldn't have any impact on the POP.
I needed to use their mailserver to be able to send as I was getting relaying problems and maybe there is where something might have gone wrong.
+Has the IP address of the server you connect to changed at all ?+
The IP address of the mailserver never changed.
I asked for an indication on where this info could be for Mail.app where I received the following answer.
+I am not sure of the file in which this stores in AppleMail. In outlook it is stored in a database file called Pop3uidl.dbx - There may be something similar to that in your file structure.+
After this answer I went to investigate further what could be done.
I went into the directory ~/Library/Mail and found amongst others the file MessageUidsAlreadyDownloaded3.
Googling this I got more confused as unfortunately when the early adopters upgraded to Snow Leopard, mail had a mishap and this was part of what was being reflected in the postings and also the suggestion to move from POP3 to IMAP to circumvent this issue.
I'm on Snow Leopard and waited until the patch was released that took care of the mail issue, to upgrade. So that is one issue less to take into consideration.
Going to IMAP is not an option either, as all of my POP mail is local and all the mail I have would not be together. Furthermore I did finally decide to integrate my gmail account into mail and this has caused my mailing to become unbearably slow (2nd issue).
Not having an option according to the write-ups, I decided to check what could be done with sqlite as MessageUidsAlreadyDownloaded3 is a sqlite DB.
Didn't get anything when trying to load the MessageUidsAlreadyDownloaded3.
As the last resort I have to delete MessageUidsAlreadyDownloaded3 and I will get all the files back which are on the mailserver according to the write-ups.
This means that I have to get rid of the already existing files that will be downloaded.
So I decided to start doing that. Then I saw that for INBOX.mbox and Sent Messages.mbox apart from the Messages directory, an Attachments directory also exists and I saw that the messages that have attachments, these attachments are kept in a directory of the name equal to the name of the .elmx, that no other mailbox seems to have these attachment directories and that for Sent Messages.mbox the attachments are incidentally copied into its Attachment directory.
Fortunately I don't have to take care of that as only my INBOX counts for the messages I have to retrieve.
I suspect that there are inconsistencies in the application as I couldn't find a correlation on the reason for having only a small portion of the sent attachment in the Attachment Directory for Sent Messages.mbox and not all.
I have not started retrieving the mails from the mailserver yet.
Is there something else I need to take into consideration before taking the jump? As I see files like DefaultCounts etc.
Do I need to take care of other files?
Something else that bugs me is that even though I deleted all the .elmx files in the INBOX.mbox of which I have a copy on the mailserver, I still keep seeing the e-mails.
Scanning the system for the elmx's that may exist for those e-mails I don't find anything. Who can explain this to me?
*Resuming I have the following issues:*
*- Is what I have done by eliminating the already downloaded e-mails including attachments “if they exist” of which I have a copy on the Mailserver enough?*
*- What could have caused my mail to become slower when implementing IMAP (gmail account) in combination with POP3?*
*- Is the inconsistency with attachments legit?*
*- A small explanation of why I have the deleted e-mails still at my disposition, while they were physically deleted (.elmx) ?*
Thanks for your reaction
Alecio

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