There is a 2GB limit on folder size.  Hitting this limit doesn't 
cause folders to disappear but will cause them to misbehave.  What you 
are describing sounds like a folder that was inadvertently moved 
(dragged and dropped?) into another folder or it was deleted.  
Another
 cause could be a corrupted HEIRARCH.PM file which maintains the 
tray/folder structure.  It it gets corrupted it can make it appear that 
folders are missing.  It can be rebuilt but any nested
 folder structure will be lost in the process.  This means that all 
folders will be at the same level  
To rebuild a HEIRARCH.PM file 
shut down Pegasus Mail.  Make a complete backup of your mailbox folder. 
 Rename the HEIRARCH.PM file located in your mailbox folder to something
 like HEIRARCH_PM.BAD.  During the next startup of  Pegasus Mail all 
folder files (.PMM/.PMI pairs) will be identified and a new HEIRARCH.PM 
file will be created.
 If you don't know the location of your 
mailbox folder use the "Info" tab located in Help | About Pegasus Mail. 
 The path to the home mailbox folder is what you are looking for.
 
 
        <p>There is a 2GB limit on folder size.&nbsp; Hitting this limit doesn't 
cause folders to disappear but will cause them to misbehave.&nbsp; What you 
are describing sounds like a folder that was inadvertently moved 
(dragged and dropped?) into another folder or it was deleted.&nbsp; </p><p>Another
 cause could be a corrupted HEIRARCH.PM file which maintains the 
tray/folder structure.&nbsp; It it gets corrupted it can make it appear that 
folders are missing.&nbsp; It can be rebuilt but any nested
 folder structure will be lost in the process.&nbsp; This means that all 
folders will be at the same level&nbsp; </p><p>To rebuild a HEIRARCH.PM file 
shut down Pegasus Mail.&nbsp; Make a complete backup of your mailbox folder.&nbsp;
 Rename the HEIRARCH.PM file located in your mailbox folder to something
 like HEIRARCH_PM.BAD.&nbsp; During the next startup of&nbsp; Pegasus Mail all 
folder files (.PMM/.PMI pairs) will be identified and a new HEIRARCH.PM 
file will be created.</p><p>&nbsp;If you don't know the location of your 
mailbox folder use the "Info" tab located in Help | About Pegasus Mail.&nbsp;
 The path to the home mailbox folder is what you are looking for.</p><p>&nbsp;</p>