I think this workaround will work with many iPad apps, since the workaround is in BoxCryptor, not a given app.
I am using Files=>BoxCryptor=>iWriter to work on encrypted Markdown files. The files show as encrypted, and I am able to edit them in iWriter, though it sometimes takes retries for BoxCryptor to download the file. But I can edit encrypted files.
But, there is no (non-workaround) way to create a new encrypted file within Files. Any new file created within a BoxCryptor folder is created as not encrypted.
I.e. If you look at the BoxCryptor iPad app there is no + button, and if you Save a new file out of iWriter it won't be encrypted.
Here is the workaround for creating an encrypted file in Files:
1) Within Files, within your folder of encrypted files, long click on an existing encrypted file, and click on Duplicate (not Copy).
2) Give the file a new name.
That duplicated file is encrypted by BoxCryptor!!
3) Edit the file to clear out the old contents.
You can make the process quicker by having an encrypted file that is empty, or with just a word in it, and name the file something like Empty. Then, when you need a new encrypted file, you only need to use the Files Duplicate command and rename it to the name you want it to have.
Thanks to this workaround, I am now able to use BoxCryptor smoothly on Mac, PC, iPad and Android. The iPad version of BoxCryptor is the only platform in which you need a workaround to create a new encrypted file.