I had the same problem with some locomotives that I downloaded. In Content Manager I clicked on the Loco giving me problems, then in the Content tab, List Dependencies, then downloaded the missing items. Turned out that most were expired, out of date, no longer used, (I forget the exact terminology) items, but once downloaded things worked fine. If I deleted those same items the problem returned. Weird.
I ended up finding similar, better locos, and deleted the aforementioned ones.
That's because the obsolete assets were still located on your hard drive and where then referenced when you removed the updates.
Trainz works this way and has since the early days.
Each asset is given a unique ID based upon a combination of your User-ID + the asset ID. This was called the Kewl User ID, or KUID system.
In the early days, assets only had KUID:xxxxx:xxxxxx... with no version. The only way to control the version was for the content creator to create a new asset and place the old KUID into an obsolete table. While this works, it's prone to errors and we've had some rather interesting results such as a factory building turning into a canal lock. All it took was a typo in the asset side of the KUID, a simple transposition of digits.
Here's a simple KUID
<kuid:511506:100309> RDG Wood Interlocking Tower - No Signs
The new method is a bit more error-proof. This is the KUID:2 system. Using KUID2:xxxxx:xxxxxx:x format. The last digit, following the last : is the version. There can be 127 versions with the last one being 126 (This is zero-inclusive). Using this format, a content-creator can update an asset, then up-version the new one by simply changing the asset-version instead of modifying the config.txt further and introducing an error.
<kuid2:132952:131602:1> SAM Elevator - Kutno, Poland
Now getting back to your issue.
In order to keep the current version, you need to delete the now obsolete assets installed. To help myself with that process, I have setup a couple of filters in Content Manager.
I first check, almost daily, for new assets.
Out of Date - No Payware.
Installed = True
Out of date = True
Payware False.
The reason for the Payware False setting is because if set to true, all payware is displayed and not the out-of-date ones!
The other filter is:
Installed = True
Obsolete = True.
This will display all the old assets that can be deleted but not any DLC or payware that was updated. Anything displayed here can be deleted.
Now with that said, there have been times when an update has broken something and removing the obsolete asset has caused an error such as a missing dependency or something to fail. The only thing you can do is delete the new version and reinstall the old one. This is done by viewing asset versions - right-click and choose view asset versions. You can then install the out-of-date version and contact the author to fix his or her update.