Before: (a rather boring generic Bachmann Industrial mogul)
After: (the only 29n2 scale locomotive in the entire world!)
Before: (two cars became one car, On30 to On2 scale)
In progress:
After:
Before:

After: (My Dad made this one..the snowplow is a personal treasure of mine, because my Dad made it.
(and my Dad passed away in '09) The original pristine LGB car would be meaningless to me..)

(Also, the value of that original LGB car has dropped from $100 to $40 over the past decade)
Before:
After:
Before:

After:
Before & After:
So..I have zero hesitation to cut things up!

because changing them is what I *want* to do with them..
I like them much better after..for me, this is a large part of the hobby..
This winter im going to start cutting up several Aristocraft heavyweight passenger cars..
"ruining the value" is of no concern to me whatsoever..because they have far more personal value after they are changed..
monetary value is meaningless to me..im not planning to sell them, so why not enjoy them while I own them?
Model trains are not an investment!

99.9% of them go down in value over time..If you want to "preserve their value" you are in the wrong game!

buy gold or silver instead.
The *only* time "future value" comes into play, for me, would be if I should happen to pass on before my wife. It could happen to any of us, at any time..
but you cant live your life concerned about that, especially when it comes to hobbies..(sure, we plan responsibility for an unexpected event like that..life insurance, etc. but disposing of hobbies simply cant be a concern, unless you are really getting up in years..)
As I get older, im already planning to downsize the train collection..
I figure by the time im 80 I will be living in an apartment, no more garden railroad, and I will sell off most of my trains before then and have only one or two remaining short trains on a shelf in the living room..If some are "less valuable" because I kitbashed them? meh..so what. We are talking differences of tens of dollars..a few hundred at most. In the big scheme of things, its simply a non-issue.
So..enjoy your trains!

get the saw out! get the spray paint out! We should buy them to enjoy them..they aren't an investment, they will never be worth more than what you paid..If you reduce the "value" of a car from $40 to $20..does it *really* matter? of course not..not if you enjoyed what you did with it.. I would argue its actually *more* valuable after you are done..because it has a higher "enjoyment value"..which is all that really matters for a hobby.
Scot