When upgrading remotely, multiple hop upgrades are needed when your agent is on version 6.9.1-504
DCS Version 6.9.1-504
When remote upgrading your DCS Agents from 6.9.1-504 to 6.9.3+ you have to first upgrade to 6.9.1-541.
Once your agent is upgraded to version 6.9.1-541 to can now upgrade to 6.9.3+ but you'll have to re-push out the IDS policy or temporarily move your agent to another security group and back again to retranslate the policy on the agent to update the repo.