Netscape 4.04 email
The following represents my experience with email folders in NC 4.04. Later versions probably do not change that much. As usual, backup any files you plan to change so that you can get back to square one if something doesn't work.

This content deals mainly with the Inbox, but the other files such as Sent, and Trash work very much alike. When you receive email, the message is stored in your Inbox. When you send email, a copy of the message is placed in the Sent folder. When you delete messages from the Inbox, or Sent files, a copy of the message is place in the Trash folder. The end result is that your hard drive may use a lot of space in storing these messages and any attachments they include.

To view the format of messages in the Inbox, click here. When you receive an email, the message is appended to the end of your current Inbox file.  The messages are appended as they arrive, so they may not be in the order indicated by the date/time. As the number of messages you receive grows, so does the size of your Inbox. When you select a message(s) and click the delete icon, you mark it for delete, and can't see it in Messenger any more, but you have merely changed its status code, and it continues to occupy space in the file. Worse yet, the delete process copies the message to the Trash file, so deleted messages now tie up twice the space on your drive. There are basically two methods used for eliminating messages you have no need for. Problems involving versions 4.72 and 4.73 have generated a third method. Method one requires you to first delete the messages you no longer need from the Inbox, Sent, and Trash files.  Since deleting from the Inbox and Sent copies the messages to the Trash file, delete messages in the Trash file last. Method two requires deleting of messages only in the Inbox and Sent files. It clears all messages from the Trash file. Method three is necessary for versions 4.72 and 4.73, and involves compressing mail folders individually.

Removing deleted messages

Method one -  In Messenger, click on the "File" menu, and the option "Compress Folders". This may be a poor term to use for the process, because many people think it means 'zipping' up the file. This option will re-build all the mail folders and remove any messages that are marked for delete. The size of the files will shrink. The SNM files will be re-built to reflect the new status of active (non-deleted) messages. Note - in order for messages to be removed with this option, they must first be marked for delete. This includes the Inbox, Sent, and Trash file messages.

Method two - In Messenger, click on the "File" menu, and the option "Empty Trash Folder". This option will completely remove all messages from the Trash folder, whether or not they had been marked for delete.  It will then perform the same process as method one, that is, it will remove all messages marked for delete from the other mail folders. Be sure to delete messages you don't want in the Inbox and Sent files first.

Method three  - Methods one and two are broken in versions 4.72 and 4.73. Using method one - File/Compress Folders - does not work at all. Using method two, the trash file is emptied, but again, it does not compress the other mail folders. To remove unwanted messages from the mail folders the following is required -

Delete any messages you don't want from the Inbox and Sent files.

If you have no need for any messages in the trash file, perform the File/Empty Trash option. If you have some messages in trash you want to keep, delete the individual messages you don't want from the trash file and do not perform the Empty Trash.

To remove deleted messages from the Inbox, Sent, and the Trash (if you did not perform the Empty Trash), you must compress each mail file individually. In Messenger, right click on the Inbox file and select the 'compress folder' option. Repeat this process for the Sent file, and the Trash file if necessary. You will have to repeat this process for any other mail files you are using.

Marking message for delete

In Messenger, access the folder (Inbox, Sent, Trash) you want to delete messages from. Select the message(s), and click the delete icon. The standard options work here. If you want to delete multiple messages, you can hold down the Ctrl key and each message you want to delete can be clicked on to select it. You can also select a message, and then hold down the shift key and select a message further down (or up) and all messages between the two will be selected. Then click the delete icon. You can also click on the 'delete' key. Clicking the delete icon or key in this manner will cause a copy of the deleted messages to be placed in the Trash file, unless it is the Trash file you are deleting messages in.  There is another option reported, but out of habit, I don't use it. If you select messages to delete, and use the 'shift' key with the 'delete' key (not the delete icon) then these messages will be marked for delete, but NOT copied to the Trash file.

Problems in mail folders
It is possible for a mail folder or its SNM file to become corrupted. When this happen, Netscape will probably abort when it attempts to access that file. It is helpful to observe what you are doing when this happens. If you are accessing the Inbox, either it, or its SNM file may be bad. The recommended step is to exit Netscape, delete the SNM file, and then re-start Netscape. When you start Netscape, if there is no SNM file, it re-creates one based on what it sees in the Inbox file. If this solves the problem, it is obvious that the SNM file was bad. Bad Inbox files aren't fixed as easily. If you suspect the Inbox itself, you should first make a backup copy of the Inbox, and you can later access it from Wordpad to read the contents if you are unable to fix it. Wordpad will enable you to view the text in a message, but an image attachment will appear as long strings of random text. If all else fails, and you have renamed and/or made a backup copy, you can delete the Inbox and its SNM file (when Netscape is not running) and brand new ones will be created upon starting. The renamed inbox can be viewed in Wordpad but, obviously,  will have limited value. Trying to figure out what got scrambled in an Inbox is tough, but it did work for me once. It was a situation where Netscape aborted only when I tried to view a particular message. I was able to open the Inbox in Wordpad, find the bad message, and delete it. I deleted the SNM file and after re-starting Netscape, the bad message and problem were gone.
The standard recommendation with mail folders is routine backup maintenance. One user claims he lost 2000 messages when his Inbox went bad. If you allow your Inbox to get that large, you should copy it to a backup folder on a regular basis, perhaps weekly. That way, if the file goes bad, you can save the bad file, restore the last backup version, and only have to worry about recovering the messages received in the last week.
Why do mail folders go bad? It is hard to say, but the primary cause is probably because they are re-written so often. There is always the possibility that a small glitch in accessing the hard drive, a timing problem, a parity error in RAM, or if Netscape happened to die while while the mail system was being used. There was a time when they wouldn't think of using RAM without parity checking but you won't find parity checking in the modern RAM modules.