Hello, everyone.
Yesterday I had a same problem, and I solved with this procedures:
I noted that if agent version in software deployment was upgraded, and I too disable Full Disk Encryption for does two tasks at the same time, the messages as "Removing FDE during upgrade is not allowed" and Deployment "Retrying" are displayed. Follow below:
Removing FDE during upgrade is not allowed

Deployment Status - Retrying
Noted the same package version for two assets, one with Deployment Status - Complete and other with Retrying.

For solved, I did:
- Previously of update your clients, disable Full Disk Encryption blade in Software Deployment and push a "Repair Client".
- Afterward Full Disk Encryption is disable, upgrade your client in Software Deployment
Obs: If only a little assets work with this issue, you can create a virtual group and a Software Deployment rule for only disable Full Disk Encryption. After, you can change for production software deployment and update.

If you have any questions, I'm available.
Asafe 😄