The trackpoint and routepoint limits are global, not per track or route. You can upload several tracks/routes but once you hit the global limit anything else will be truncated.
I'm sorry, but this is incorrect and the page you linked to above also gives incorrect information.
The Etrex C series (including such as the Vista HCx) can store up to 10,000 'active route' trackpoints
plus up to 20 'saved' tracks of up to 500 points each, ie another possible 10,000 points in total, stored internally. See pic below. The 20 'saved' tracks can be any combination of tracks uploaded to the GPS and recorded tracks saved on the GPS, but each one cannot exceed 500 points. This is all regardless of anything that may be archived to the SD card.
I can't help with the OP though - looks very strange. It is true that if you upload a Track to the Garmin that is over 500 points - you won't see any error message. The first you'll know about it is when you fall off the end of the Track. So my guess is this is most likely what happened, despite you thought you'd filtered everything.
[edit to add -
Screendump from a 'full' Legend C - ie an older and more limited model - much less storage ability than the Vista HCx.
The red bar shows a full Active Log of 10,000 points.
The list shows the last few of 20 additional stored Tracks. See the scrollbar to the right shows this is a longer list.
Trust me, there are 20 of them (which is why 'Save' is greyed out - it's full), and each contains 500 points.