Reproduction steps:(Gif in the Edit)
1) Open attached project.
2) Go into playmode, select any sprite in Asset window.
3) In Inspector hit Sprite Editor and in the upper left corner change Sides value.
4) Either stay in the play mode or stop it and close Sprite Editor window.
5) Hit apply to apply changes made before.

Note: were no auto popup window for Change Shape in Sprite Editor in 5.2 - The issue came with its implementation 5.3.

Reproduced with: 5.4.0b11, 5.3.4f1
Does not reproduce with: 5.2.4f1