I believe you have already explained. It seems you use an IMAP mail account to remotely access emails stored on the server. You also use your iphone to connect to server. In Thunderbird, you subscribe to see folders on the server. Imap mail accounts access those subscribed folders and download headers to Thunderbird. When you select to read an email, it is retrieved from the server and stored in a temporary cache to faciliate reading. It is not downloaded and stored in thunderbird. These emails are stored on the server until you delete/move them off the server. re :''then transfer them to my iPhone and archive them.'' By this I presume you mean iphone accesses server and moves emails off server onto iphone. Archive where? If you are removing emails off the server then they will not be available, so the already downloaded headers get displayed but there is no content and you see the message "This message has not been downloaded from the server". This could mean the index is not reflecting the true information on the server. Right click on folder and select 'Properties', then click on 'repair folder' button. If the emails were not moved off server then perhaps they were moved to another 'Archive' folder and Thunderbird has no knowledge of that folder - maybe you need to subscribe to see it.