I have a similar workflow, but none of the tools worked for me:
I have planned a cylce trip of ~3000 km (~50000 gpx points). I watch it on different maps and in Google Earth and sometimes I decide that
an alternative way might be better. So I create a new gpx track for that alternative and now I want to replace the corresponding part
of my old trip with the new one. It is possible with GPX Editor [1], but quite a lot of mouse clicks are needed to remove overlaps and
join the parts, and this tool tends to make errors when combining parts :-(, so I sometimes use a simple text editor to do that.

I should be rather simple to code a (batch) program which does this, maybe I’ll do that before I plan my next trip.

[1] https://sourceforge.net/projects/gpxeditor/?source=directory