OK, here's the scoop on this, but don't blame me if it doesn't make sense.
First, I'm sure the problem isn't Eric's update, but another DTG mystery.
As of today, the route has the following attributes:
I'm the original owner of Donner Pass, dating back to when it was first released. At one point, certain scenarios stopped working because there was an update - not sure when - that changed the track geometry.
Route Number = 32. Within folder 32, I only have Route information & Scenarios folders, Main content.ap & route properties.xml.
I know at one point, I opened the .ap file using RW Tools, so I'm not sure why the exploded folders aren't present.

Did DTG update Donner Pass recently?
I haven't done a nasty verification of game cache in a zillion years, because I don't need all my modifications erased.
As soon as Eric's Donner pass update is added, poof all the checkmarks go down the tubes.

Luckily, there's a posting on this forum about how to retrieve the checkmarks, by using a backup SDBCache.Bin file.
The checkmarks return when I delete the update files, and substitute the old SDBCache.bin file.
I tried using the route properties.xml file from the working backup, but this didn't help the checkmark situation.
Rob

Let's Go Mets!