I read on some forum, gmail uses "ALL mails" folder. Thunderbird subscription system download both the mails, so i the subscription list I unchecked the All Mails and left inbox checked. This solved mine problem, I hope that was it.
The file \Data\profile\Mail\pop.[mailserver].[domain]\popstate.dat file is what keeps track of which emails have already been downloaded from the POP server.
An example on my Windows XP Home PC is:
C:\Documents and Settings\Alan\Application Data\Thunderbird\Profiles\qn5qd3de.default\Mail\pop.att.yahoo.com\popstate.dat
# POP3 State File
# This is a generated file! Do not edit.
*pop.att.yahoo.com AWehmann
k AHfVimIAAFFZTwJOOAAQHz0XYU8 1325822549
k ALnPjkQAARslTk0SJwOBFFSXUwk 1313674828
k ALbPjkQAADijSiRISQK9whTL178 1243891806
k AK/VimIAAXI5TwSSMQM8WDKNut0 1325822555
k ALDVimIAASYOTuZNwgVwMgSXZN4 1323792415
k AN7VimIAAM1uT0ZHUA1JGhbBzms 1330020393
b AODVimIAAQzKTuDXaAISoH6BC8M 1323402949
There are more entries, but I don't show all of them.
The column #2 has email IDs, column #3 has the email dates in unixtime format (use a tool to convert to human-readable or back).
By deleting appropriate lines you can make Thunderbird re-download those emails.
In your case, as Thunderbird has the IDs already, it should not re-download these emails.
In the case of Gmail things are somewhat different. With default settings the Gmail POP server only offers newly arrived emails. If there are none, then the popstate.dat file is emptied out, since the server reports that there are no emails available for download from the server.
Best Answer
In Thunderbird (depending on your version), look for an icon with three stacked horizontal bars (Application Menu). Click on it, then go to the following: Options... (click the dropmarker) > Account Settings... > Synchronization & Storage > Message Synchronizing > checkmark the "Keep messages for this account on this computer" > Advanced... > checkmark any folders you wish to cache messages for offline use. Make sure you have enough available hard drive space.
Caching messages offline will store in your hard drive a copy of all messages. All messages will be downloaded the first time in the folders you select for offline use. Then Thunderbird will download only new messages after that.