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Syncthing encrypts the data, so it will be encrypted when being transferred. However, Aegis can export the vault into an encrypted file, too. So the vault file you will be transferring over an encrypted channel is encrypted itself as well. That means that the vault is secure even when at rest on some device.
You are mistaking KMail (desktop client by KDE) and K-9 Mail (Android client that is being rebranded into Thunderbird for Android).