Hello, I was just about to post this question here as the information available was very limited (and the one piece of guidance I did find was incorrect) but I figured out the fix and wanted to share.
The problem was that I had two UV maps in blender, "head" and "body," each with their own assigned material, but when exported to Substance Painter (as an FBX of course), it recognized both UV maps, but only recognized one island, the head.
and due to negligence on my end. The cause of the problem was that my head was unwrapped in both the UV maps. So somehow this caused Substance Painter to only recognize that island, between both of the maps.
The fix was fairly simple. All I had to do was select the common island between both maps (in this case, the head) and weld it down on the desired UV map. Since I didn't want it to be on the body UV map, I selected the island (hover mouse over island>L key), welded it (shift W>Weld) and pinned it (P key). From there it exported just fine and Substance Painter now recognizes both of my UV maps and all of their respective islands. Now you probably have a considerable vacant space in your UV image, which is not making an efficient use of space if you plan to texture or paint them. You can resolve this by selecting all islands (A key) and packing islands (UV drop down>pack islands).
If this doesn't work make sure you have materials assigned to your UV maps as well. Just create a material, give it a color, select an island, and assign it.
Replies
Substance will take each material as a texture with its uvs and let you work from there.
It sounds like you have the head on both UV maps, it should only be on one. Otherwise you're trying to apply two textures to the same area at the same time.