In my long experience of using Trainz, almost as long as yours, I do not recall ever seeing such an issue.
It would help if you could clarify a few points.
"It is therefore necessary to have each and every spline in working order before saving" - what exactly do you mean by "working order"? In my experience a spline is either present or it is not. The only feature of non-track splines that is important is height and that is subject to individual preferences, as is whether or not the spline points are joined or not.
What does Content Manager say about your route? Missing assets, faulty?
Can you give some specific examples? Kuids would be most helpful.
Development: Trainz Plus - b117699, Win 10, 16GB, RTX 3060Ti
Testing: Trainz Plus beta - b117669, Win 11, 16GB, RTX 3050Ti