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Without going into a lot of detail, you are seeing an incompatibility with MTP and the Windows file system, which is by design. MTP does recognize file changes on your MTP device until it is re-indexed. I am working through the issues to try and develop a knowledgeable guide for using file transfer with MTP, so bear with me. For the moment disconnecting your tablet from your PC and restarting your tablet will force re-indexing of the internal storage and show the missing files. Note you may have to re-start your pc as well. Any feedback, you can provide will help me with developing a guide.
Also as an temporary work around you could upload the TWRP files to Google Drive or another cloud based storage service.EDIT- Another workaround is, if you have a USB Flash drive (thumb drive) use stick mount and save or transfer the files that way.
@ norcal618Great feedback, I have been working on permissions in regard to access using MTP. Can you post the permissions for your new TWRP folder?
I recently switched over to team win recovery from cwm. I do like the ui and functionality way better then cwm. The problem I'm having is that I cannot access my back up files from my PC via USB. When I use the file browser that is built into twrp I can see the back up files in the twrp folder. When I plug my tablet into my PC via USB and open the twrp folder it is empty. Also when I open the twrp folder in es file browser it is empty there too. I would like to store the back up on my PC rather then on my tablet. Am I missing something? I was having this same problem with titanium with backed up apps so I upgraded to the paid version and uploaded my back ups to Google drive. After that I looked in the titanium back up folder again on my PC and all the sudden the files were there when before they were not. Its very frustrating. Please help.