Hi and welcome to the community!
I’ve had a similar problem in the past with importing individual activities from Garmin, and I tried to get a bit forensic with it so I’d refer you to my post on this thread and replies with James (perhaps this is even what you were referring to): Show Delete Activity Delay in Status - #13 by kevincharlespels
In that thread I am editing my messy GPS data with routeconverter just like you, and from that thread realized that creating new nodes that have corrupted timestamp data can make weird lines that mar the trace/lifemap. Editing the text/code in textedit is extremely tedious, so my working solution has been to never add new nodes to a trace, only drag existing nodes to the tracks I actually ran and delete others as needed. In this way, there is never an out-of-chron GPS timepoint. After all, the point of this is to have an accurate trace, the other metadata is superfluous for CS and I can delete the activities from Garmin once they’re in CS. I will finally add that I have only worked with gpx files and not tcx files, but I don’t know enough about the difference between gpx/tcx to say anything further.
Finally, not possible to mark individual nodes as complete but if you did literally run them and are already using routeconverter, just drag your gpx trace closer to the node to reflect what you did in reality.
Cheers