Yes — by design, not by accident

Eagle's own support documentation says so plainly: Eagle copies files to the library when importing, rather than just creating index links to the original files. Once an image or video is imported, the copy inside Eagle's library is the one the app works with — the file you dragged in still exists at its original path, but Eagle isn't tracking that path as the working copy anymore.

Whether that's a problem depends entirely on what you were already doing with the folder you imported from. If it was a scratch folder you meant to clear out anyway, the copy is just where the files end up living. If it was a folder you were relying on as the real one — synced to another machine, backed up on its own schedule, shared with a collaborator — the copy quietly becomes a second thing to keep in sync with the first.

What that means in practice

A few consequences follow directly from copying rather than indexing:

• Every imported file exists twice on disk — once where you originally kept it, once inside Eagle's library folder — until you clean up the original yourself.
• Moving or renaming the original afterward doesn't touch Eagle's copy, because the two are no longer the same file as far as the app is concerned.
• The library folder becomes the thing you have to back up. Losing it loses Eagle's copies, tags and ratings even if the originals still exist somewhere else on the same drive.
• A large import roughly doubles the disk space it needs, at least temporarily, since nothing is deleted automatically as part of the import step.

Why this is worth checking before you commit to a library

The copy-versus-index question isn't a detail to skim past — it decides where the file you actually care about lives once you've been using the app for a year. With a copy-on-import design, the library folder itself becomes the canonical copy, and the original you dragged in is just the source it was made from; deleting or reorganising the original afterward doesn't touch anything Eagle is showing you, because Eagle stopped watching that path the moment the import finished. That's fine as long as you remember which copy is which, and it becomes a real question the day a backup only covers one of the two locations, or the day you assume tidying up your source folders is harmless.

The alternative

Not every reference tool works this way. Coii Ref takes the opposite approach: it reads the folders you already have, keeps its database, thumbnails and canvases inside the folder you pointed it at, and never copies, moves or renames a single original file. There's one copy of each file, in the place you already keep it, whether or not you ever open the app again.

Which approach is better depends on what you want — Eagle's copy-on-import gives it a self-contained library independent of where files started out, which the full comparison covers in detail along with the features Eagle has that Coii Ref doesn't. If keeping exactly one copy of every file, in your own folders, matters more than a self-contained library does, see what else people move to when Eagle's storage model stops fitting.