I have to say, I was surprised that my test on the 'clean' secondary PC worked OK first time; I remember it being quite difficult to set up my personal default apps on my main PC a while back. You have my sympathy! Are you running the very latest versions of W10 & 11? As I said initially, W11 was heavily criticised on release for its clear attempts to prevent users from setting anything other than MS default apps; I wonder if one of the reasons I found it easy with my test is because later versions...
This behaviour persists after an unmount/mount of the the VC volume, and a shutdown/start of the PC, and mount of the VC volume.
LibreOffice Writer launches OK whenever I click on the .docx file now. I wonder whether your issue may be something to do with where LibreOffice is installed?
I can't reproduce your issue with LibreOffice Writer. I created a 25GB test VC volume on a secondary W11 PC that has no 'Office' sofware on it at all, on the E: drive, and mounted it to H:, and installed LibreOfficePortable to folder 'LibreOffice'. (Note: I never accept the pointless default behaviour of 'Portable Apps' installers - .paf.exe files - of installing the sofware in a subfolder of the folder I say I want it installed in, using the apps name ie 'LibreOfficePortable' in this case.) I then...
What operating system/version are you running? And are you using 'Portable Apps' versions of Chrome and Libre Office? I may be able to help troubleshoot this by experimentation - seeing if I can reproduce your issues, and what steps might resolve it. I have run almost my entire computing activites for years now using portable software installed in VC container files. I use Firefox as a browser, but have Chrome available to test; I use LibreOffice. My first thought is, W11 is much more 'hostile' to...
Is the drive on which the files are stored an external portable drive? Is the drive formatted NTFS, and was NTFS used when setting up the encryption?
You don't say what type and size of files are 'missing' in Windows, but do you have Linux set up to show 'hidden' files, but Windows to hide them?
What did you actually do? a. Encrypt your E: drive (a whole drive, or a partition on a drive)? b. Create a file container (with the .hc extension)? On what drive? c. Or both, ie encrpyt your E: drive, then mount it and create a file container on that? Can't possibly begin to assist you until you clarify this. It's also necessary to provided a relevant screenshot, ie of Windows Disk Manager, showing your drive configration.