I created two Aperture libraries from one large library. Some of the photos in library

I created two Aperture libraries from one large library. Some of the photos I want to keep in library #2 are in the trash of library #1.  If I empty the trash of library #1, will it affect the same photos that were moved to library #2?  I moved over 2,000 photos to create library #2.  Their names are showing in the trash of library #1. 

Are your images referenced or managed? If your partial libraries are referencing the same original files as the library you exported them from, be careful. Deleting the orignal on one library #1can delete it from the  library #2. But if your originals are managed by Aperture inside the Aperture library, you can delete them.
I moved over 2,000 photos to create library #2.  Their names are showing in the trash of library #1.
If you are not sure about referenced or managed, select one of the images you want to keep in the library where they are not in the Trash, then use the command "File > Show in Finder". If you can reveal them in the Finder, they are referenced and probably are shared between your libraries.
Or turn on "badge referenced files" in the Preferences > Appearance settings. Then your referenced images will show arrow badges.

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