In order for us to better investigate this issue you need to add a little more non-personal information.

Please add the troubleshooting information to your post To find the Troubleshooting information:

• Open Help (or click on three-line-icon and select Help)
• Choose Troubleshooting Information
• Use the button Copy to clipboard to select all. Do not check box "Include account names"!
• Paste this in your post.

Application Basics

   Name: Thunderbird
   Version: 52.4.0
   User Agent: Mozilla/5.0 (Windows NT 10.0; WOW64; rv:52.0) Gecko/20100101 Thunderbird/52.4.0
   Profile Folder: Open Folder

             (Local drive)
   Application Build ID: 20171004092449
   Enabled Plugins: about:plugins
   Build Configuration: about:buildconfig
   Memory Use: about:memory
   Profiles: about:profiles

 Mail and News Accounts
   account1:
     INCOMING: account1, , (pop3) promail.ptd.net:995, SSL, passwordCleartext
     OUTGOING: , promail.ptd.net:587, alwaysSTARTTLS, passwordCleartext, true

   account2:
     INCOMING: account2, , (none) Local Folders, plain, passwordCleartext

 Crash Reports

 Extensions
   Lightning, 5.4.4, true, {e2fda1a4-762b-4020-b5ad-a41df1933103}

 Important Modified Preferences

   Name: Value

     browser.cache.disk.capacity: 358400
     browser.cache.disk.filesystem_reported: 1
     browser.cache.disk.smart_size_cached_value: 358400
     browser.cache.disk.smart_size.first_run: false
     browser.cache.disk.smart_size.use_old_max: false
     dom.apps.reset-permissions: true
     extensions.lastAppVersion: 52.4.0
     font.internaluseonly.changed: false
     font.name.monospace.el: Consolas
     font.name.monospace.x-cyrillic: Consolas
     font.name.monospace.x-unicode: Consolas
     font.name.monospace.x-western: Consolas
     font.name.sans-serif.el: Calibri
     font.name.sans-serif.x-cyrillic: Calibri
     font.name.sans-serif.x-unicode: Calibri
     font.name.sans-serif.x-western: Calibri
     font.name.serif.el: Cambria
     font.name.serif.x-cyrillic: Cambria
     font.name.serif.x-unicode: Cambria
     font.name.serif.x-western: Cambria
     font.size.fixed.el: 14
     font.size.fixed.x-cyrillic: 14
     font.size.fixed.x-unicode: 14
     font.size.fixed.x-western: 14
     font.size.variable.el: 17
     font.size.variable.x-cyrillic: 17
     font.size.variable.x-unicode: 17
     font.size.variable.x-western: 17
     mail.openMessageBehavior.version: 1
     mail.winsearch.firstRunDone: true
     mailnews.database.global.datastore.id: 3b4c786b-abdc-4e72-b51e-3813c3c96b3
     media.gmp.storage.version.observed: 1
     network.cookie.prefsMigrated: true
     network.predictor.cleaned-up: true
     places.database.lastMaintenance: 1511101641
     places.history.expiration.transient_current_max_pages: 122334
     plugin.importedState: true
     security.sandbox.content.tempDirSuffix: {285fbe94-c192-4991-a0b6-f2a93e6a3036}

 Graphics

     GPU #1
     Description: Intel(R) HD Graphics 520
     Vendor ID: 0x8086
     Device ID: 0x1916
     RAM: Unknown
     Drivers: igdumdim64 igd10iumd64 igd10iumd64 igd12umd64 igdumdim32 igd10iumd32 igd10iumd32 igd12umd32
     Driver Version: 22.20.16.4771
     Driver Date: 8-13-2017

     Features
     Direct2D: false
     DirectWrite: true (10.0.15063.674)
     WebGL Renderer: Google Inc. -- ANGLE (Intel(R) HD Graphics 520 Direct3D9Ex vs_3_0 ps_3_0) -- OpenGL ES 2.0 (ANGLE 2.1.0.2a250c8a0e15)

     AzureCanvasBackend: skia
     AzureCanvasAccelerated: 0
     AzureFallbackCanvasBackend: cairo
     AzureContentBackend: skia

 JavaScript

 Incremental GC: 1

 Accessibility

   Activated: 0
   Prevent Accessibility: 0

 Library Versions

     Expected minimum version
     Version in use

     NSPR
     4.13.1
     4.13.1

     NSS
     3.28.6
     3.28.6

     NSS Util
     3.28.6
     3.28.6

     NSS SSL
     3.28.6
     3.28.6

     NSS S/MIME
     3.28.6
     3.28.6

I have this problem also. The number of items available to me are *much* less than the total size of my TB mail (in excess of 4 GB; MozBackup ceates a 18 GB backup). All of my folders listed by year from 2004 to present have disappeared.

Is this just an issue of indexing ?