Reproduction steps:
1) Open project I have attached.
2) Open Sprite Packer window and proceed to Sprites folder.
3) Select "GrasslandColor3@128x128" sprite sheet and notice there is Packing Tag set in inspector.
4) In the Sprite Packer window hit "Pack" button - should work fine.
5) Move "GrasslandColor3@128x128" to Resources folder.
6) In resources folder select sprite sheet and change Packing Tag and save it.
7) Repeat step 4 - Atlas should not be formed this time.

Expected behavior: Sprite atlas is generated.
Actual result: Previous sprite atlas disappears and new one is not formed.

Note: Moving to any other folder works just fine.

No workaround for those who need sprite sheets in resources folder in order to import them at runtime or to use asset store plugins that require them to be there.

Reproduced with: 5.3.2p2, 5.4.0b3, 5.2.4f1, 5.1.4f1