Rules to Flag a node referenced by Commerce Order Line Item
I believe you'll either need to access the node ID from the line item entity using a loop within the Rules UI or what I think a simpler way would be to create a custom Rule that accomplishes the same task.

Something like:
Event:  order is completed. I guess you could use order paid in full.
Conditions:  Here is where a custom condition would come into play.  You'd need to dig through the order line items to the user-selected node, and then pass that node_id to the Rules action as a parameter.  Note:  you could also do this entire check within the action and then programmatically set the flag to avoid passing the node_id as a parameter.
Actions:  Set a flag on a node.  (The node parameter).