You can find most of the information regarding how the data is scanned and sent to Lansweeper here: https://www.lansweeper.com/knowledgebase/lsagent/#heading4
In short, LsAgent will send the data to the cloud relay server via HTTPS. While your data is on the relay server waiting for installation to fetch it, it is encrypted using a encryption key only we have. Lansweeper will fetch your data via HTTPS again to get it into your installation.
Just to make this clear, the encryption on the cloud relay server was added to ensure that even in a worst case scenario, the data stored on it is safe. The encryption key used to encrypt the data is not accessible to any third parties and will in no case be used to decrypt customer's data.
Lastly, as soon as data has been retrieved by your local scan server, it is removed from the cloud so no data is kept longer than needed.