Overwriting and existing texture via saving with Photoshop causes Minecraft to not recognise the texture, and causes the model to load in with a missing texture. 

Reproduce:

1) Make a working custom entity with PNG texture

2) Load into world and observe working texture

3) Open texture in Photoshop, edit some pixels, save as..., overwrite texture

4) Close and Open world

5) Observe missing texture

Work around:

1) Delete the PNG texture file

2) Use Photoshop to save the file as a brand new PNG

3) Close and open world

4) Observe that texture is now fixed

It is clear that Minecraft is hiccuping on some sort of data associated with overwritten files from Photoshop.