Agent IDs are assigned sequentially, and an Agent gets an ID on its first connection to the LEM appliance. This ID is encoded in the certificates that the Agent gets on first run, so if you're getting duplicates that would suggest that the Agent install folder was copied to multiple machines (perhaps VDIs?)
We have directions on using LEM agents in a Windows Image, so you may need to look at that and resolve the duplicate agents by resetting Agents to a "first run" state by deleting their certs.
Directions on resetting agents, you may need to look in SysWOW64 instead of System32 on new systems (section "Reset the LEM Agent Certificate"): Troubleshoot LEM agent connections
Using the LEM Agent in a Windows image: Include the LEM Agent in a Windows image - SolarWinds Worldwide, LLC. Help and Support