What is likely happening is that the game reads its default scripts from the libraries.big. I don't know necessarily why your imported scripts have seemed to disappear, but I've found the various libraries to be a bit buggy over all. The easiest way to go about working on them is to extract the entire libraries.big and put it into a new libraries folder inside the main BFME directory, then remove the libraries.big entirely from the directory. Then you can edit and change things there and the game will detect those as the original ones. If you leave the libraries.big in, the game will tend to overwrite your changes by defaulting to the libraries contained in the big, so it's best to "force" the game to use the ones you want.
Also you probably have noticed that the default imported scripts that many of the libraries have don't behave the same as normally imported scripts do. But since you're creating a new library for your elves you will have to just try and mimic it as best you can by manually importing the scripts from all the necessary libraries (after you have edited them to include your new data for your faction) into your skirmish libraries.
Ideally if you bypass the libraries.big and change/import all the necessary things, then your new skirmish libraries should function correctly.
Not to mention it's easier to test your work this way since you can make quick changes to the scripts and it will be read correctly in game without having to compile them into your mod every time! Just don't forget to temporarily move the libraries out of your mod otherwise you will start having overwriting issues again. Just edit them in the directory folder until you're satisfied with your progress/results, then take those and compile them into your mod and put the libraries.big back. And you should have no issues then.
https://www.twitch.tv/vileartist - Yes shameless self-promotion
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"Old modders never die, they just fade away" ~ Hostile