Yomao Spinebot's answer doesn't directly address your question, so in that sense it's not ideal. However, it's not entirely wrong either. You seem to be manually duplicating atlas files, but that's actually unnecessary.
For cases like yours, where the runtime warns about missing corresponding atlases during import, there's spine-unity, for example. With spine-unity, if you first select “Import without atlases” to import the skeleton data, then later set an Atlas Asset in the Skeleton Data Asset's Atlas section, it should load correctly as long as the paths to each image described within the atlas file match those held by the skeleton data:

Skeleton Data Asset immediately after import:

After manually adding the corresponding Atlas Asset:

Similarly, in other runtimes, you can specify the corresponding atlas file either through the GUI or via code. If you want to know the method for the runtime you're using, please tell us which runtime you're using.