2. Combining objects with different textures and UVs:
The problem isn't the file name but the materials defined by .mtl and .obj. If different source files use the same material label you'll run into issues.
3. Your special example:
Your problems are not related to UVs in any concern. You should take a closer look at SELECT options to avoid errors you need to repair later on (and if you don't repair these errors properly risk crashes). Besides SelectVisible there are options as:
- A nice trick to check if you've missed some region is to run Modify/SmoothBoundary (but don't Accept). As it highlights selection boundaries you see what you've missed.
- There's ExpandRing and ContractRing. ExpandRing adds a loop of neighbour faces to the selection while Contract shrinks. Now you can get rid of tiny missed areas by growing the selection X-times and shrinking it X-times.
- There are RMB-drag Expand modes (requires Meshmixer navigation mode): GeodesicDistance and CreaseAngle based (ColorSimilarity is based on PerVertexColor).
- Instead of discarding a selection the saver way if you are not sure to have selected all you want is to Separate the selection to a new object X. If there were missing regions go back to the source object, select the missing region and Separate it to an object Y. Now Combine X and Y and run EDIT/CloseCracks to weld.
- If there are watertight intersecting objects A and B. A is the active object. Now in SELECT double clicking at B selects all faces of A within B
- DoubleClicking a FaceGroup selects all faces of that group. You need to set GroupColor as MeshColorMode to see them.
Sharp edged objects (as your interior surface) are ideal for that. Run EDIT/GenerateFaceGroups and use its EdgeAngle Mode. Define the AngleThresh ( higher results in less groups) and SizeThresh (higher results in less groups) until you get a meaningful result. Now you have groups you can easily select.
.....
Not knowing your partial shells:
Separate your two shells to two objects.
On the outer (textured?) egg surface select its outer surface, invert and discard its inside (if there's any). Close the open boundary using Inspector. This should result in something like a solid egg shaped half sphere.
From the inside object (use FaceGroups for that) select the groups pointing to the inside. Invert/Discard. SelectAll and FlipNormals. Close the upper hole and extrude this new surface a little bit . This should result in some negative part.
Activate the outer surface object first and (holding shift) add the inside object. Now run BooleanDifference.
This should be a 2min job you are familiar with the toolset.