The IMAP system works by always showing you what is on the server, there is no local copy (apart from what is cached). Flags such as Read/Unread, etc. are also stored with each email on the server so everybody sees the same thing.
However one thing you could do is train everybody up so they only use the Reading Pane to view the messages and then set the Reading pane options (Options/Mail/Outlook panes/Reading pane...) so the item is never marked as read when viewed there.
If anyone opens the email in a separate Window it will still be marked as read but they could also mark it as unread again.
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
POP is working as designed, here. If you access a mailbox via the Post Office Protocol, you are expected to be transferring it off the server to storage of your own. (RFCs 1081 and 1939 both make this point explicit in their introductions.) From the server's point of view a message that has been
RETRieved but not yetDELEted is indeed "read" by the POP client.If you are using the Post Office Protocol to keep mail on the server indefinitely, then you are in fact abusing the protocol. POP has never required that maildrops hold mail indefinitely. Indeed, RFC 1939 ยง 8 is clear about the fact that servers are quite free to outright delete messages that you've retrieved but not deleted yourself, let alone simply mark them as read. The Post Office Protocol is, as the name suggests, a protocol where mail is held at a "post office" drop point, from which you collect it and take it away whenever your MUA is connected to the network.
So your question is essentially unanswerable. You are asking how to make POP not work as designed. Of course, this is another case of picking the unsuitable tool for job and then asking how to modify the tool so that it works. If you want a protocol that's designed around the paradigm of having a remote mailbox maintained on a mail server (rather than POP's last-leg-of-the-store-and-forward-chain paradigm) which is accessed by multiple client MUAs, then use IMAP. It's that simple.