is this a CT issue or a Garmin issue? Is it possible that the "new" version of the route is not being copied over because Connect thinks it is already there? The simple way to test this is to change the route in an obvious way on CT, save it under the original name and a new name. Are both the same on Connect?

Apologies if you've already tested this.  

I have indeed tried deleting the route in GC and doing as you've suggested, with no luck. I need to investigate properly but it also appears that on sending the route to GC that the location of the Course Points are not excatly in the same position as the Via Points. 

I did have some success in deleting and adding new Course Points to the route in GC after downloading the CT route as a GPX file and uploading it in GC instead of 'sending' it across from CT.

Of course, on testing on a short route I have not had an issue! The two routes I have had an issue with have both been multiday tours with overnight stops that I then saved into different days.

Apologies if I'm suggesting what you have already tried..... but it's not clear to me from your answer. 

Take the "long route" you already have in CT. 

Change it dramatically, not just a viapoint note. 

Save it as the "old name" and a completely new name. 

Do whatever it is you do to bring both into Garmin Connect. (Don't delete anything in Connect).

Then look to see if they are both the same on Connect. If they are not the same that suggests the issue is on the Garmin side, no?

Alternatively, have you considered bypassing Garmin Connect and just sending the gpx/tcx file directly to the unit (either Bluetooth or cable)?

As a final alternative, there are a number of downloading options from CT. Are you sure you're downloading the same format every time?

Or, try downloading a different format. That may help. 

Yes, I've done those steps. 

I moved the start & end of the course a couple of km away. Saved it as a new route. Sent it to gamin connect with the errant Course Point still showing. Tried downloading the GPX file and uploading it to CG connect with the same results. Tried a TCX file but no Course Points show when uploading that file format to GC.

Here's the route in question: https://cycle.travel/map/journey/465912

My observation re: the position of the Via Point / Course Point differing is confirmed as well:

Perhaps I'm dim but I'm seeing two separate issues:

1: Viapoints/Coursepoints "staying" in GC:

A Viapoint with note attached, created in CT will appear in GC when the route is uploaded to GC the first time. However, if that Viapoint is deleted in CT, the edited route uploaded to GC, the Coursepoint (with attached note?) stays showing in GC?

2: The physical location of CT's Viapoints and GC's Coursepoints do not match up

If my understanding of 1 is correct what happens in an extreme case, say London to Edinburgh via Viapoint Bristol. Does GC continue to show London to Bristol to Edinburgh even after deleting Viapoint Bristol?

In relation to 2, I wonder if there's some automatic adjusting going on whereby CT is showing the location of the ViaPoint but GC is showing the location where the notification of the Viapoint first appears for display on the unit? 

Tried a TCX file but no Course Points show when uploading that file format to GC.

In case you're not aware, there are two different formats of TCX available to download from CT (available under "More Download Options")