Hi mhahn ,
You are right about folder structure being different.
However, removing iotkit-agent will result in loss of registered data (sensors, device token...).
That's why you should follow upgrade instruction - if the agent version is older than 1.6.0 (different folder structure) - you should follow also migration instruction enableiot/iotkit-agent · GitHub (which is also mentioned in the upgrade instruction itself).
Hope it helps.
Regards,
Joanna