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Thank you for your post!
Once a file is encrypted by FileMaker Pro Advanced (or in FileMaker Cloud) it will continue to be encrypted in future versions unless you intentionally remove encryption using FileMaker Pro Advanced.
If you are using FileMaker Server, we would highly recommend using a custom SSL Certificate. For information on this process in FileMaker Server 16, see Configuring security for FileMaker Server 15 and higher
I'm also going to move this thread from the FileMaker Community Feedback Space (which is specifically for input on the Community itself) to the Discussions Space where you should receive more views and potentially more feedback on this topic!