From a quick read of your posts it is clear that you lack an understanding of some of the Trainz internal workings with regard to obsoletes.
When an asset is upversioned and requires a library, all parts of the updated asset must be updated and the old versions deleted where possible. (solves the 'X' not found in 'Y' error')
Run 'out of date' filter, select all and right click to select 'view asset versions', a new window will open then sort on status and download any 'available for download. This ensures that ALL out of date assets are found including built-in and payware. After all the updated assets are downloaded, make a filter 'obsolete=> AND NOT => built-in', run the filter and delete ALL obsolete assets. (usually only installed from DLS and modified)
In the current beta, I had a large number of 'missing dependencies', which I fixed by clicking on the routes CM icon in the route list in-game and downloading anything 'available for download'.
Some regular maintenence of your database is needed to keep trainz running well and minimise problems.
Please don't blame N3V or the Trainz software when things don't go right for you, explain your problem and ask for a solution is always the best way to get the right answer.
Sometimes our expectaions don't match the software's capabilities, but, most times the error is between the chair and keyboard.
cheers
Graeme