Bugzilla

> couldn't find the folders which disappeared there. They were All sub-folders. 
> All the sub folders under Paid disappeared example: Ebay>Paid>

I'm not sure whether you checked the following information, so I've provided some info just in case.

In profile folders, in the mail account, you should see :
'Ebay.sbd' folder  which contains subfolders
'Ebay'  no extension mbox file
'Ebay.msf' index file

In the 'Ebay.sbd' folder, you should see:
'Paid.sbd' folder which contains subfolders
'Paid' no extension mbox file
'Paid.msf' index file

If the 'Paid.sbd' folder is missing then so are all the subfolders.
If the 'Paid.sbd' folder is visible, BUT  the 'Paid' mbox file is missing then Thunderbird will have no knowledge about any subfolders which are in that 'Paid.sbd' folder.  This means you need to create an mbox file called 'Paid'

Exit Thunderbird if it is running.
Create a new Text Document and call it 'Paid' - exact same spelling as the 'Paid' shown in 'Paid.sbd'
This creates a 'Paid.txt' file - now rename that file, by removing the .txt extension, it will warn you, but you do want to do it.
This creates an mbox file.

Start Thunderbird.

> couldn't find the folders which disappeared there. They were All sub-folders. 
> All the sub folders under Paid disappeared example: Ebay>Paid>

I'm not sure whether you checked the following information, so I've provided some info just in case.

In profile folders, in the mail account, you should see :
'Ebay.sbd' folder  which contains subfolders
'Ebay'  no extension mbox file
'Ebay.msf' index file

In the 'Ebay.sbd' folder, you should see:
'Paid.sbd' folder which contains subfolders
'Paid' no extension mbox file
'Paid.msf' index file

If the 'Paid.sbd' folder is missing then so are all the subfolders.
If the 'Paid.sbd' folder is visible, BUT  the 'Paid' mbox file is missing then Thunderbird will have no knowledge about any subfolders which are in that 'Paid.sbd' folder.  This means you need to create an mbox file called 'Paid'

Exit Thunderbird if it is running.
Create a new Text Document and call it 'Paid' - exact same spelling as the 'Paid' shown in 'Paid.sbd'
This creates a 'Paid.txt' file - now rename that file, by removing the .txt extension, it will warn you, but you do want to do it.
This creates an mbox file.

Start Thunderbird.

Please report back on whether info helped.