I've done as you've suggested and controlled for vanilla vs altered mesh. I also wiped my installation and started from scatch. Here is what I found:
Vanilla meshSteps Used:1. Copy and Paste Marine_00 and Marine_00_Explore into a pre-created DLC folder (I utilized the DLC_CON_AshWar folder in this instance)
2. Start up Texplorer and rebuild the tree with only DLC_CON_AshWar selected
3. Navigate to BIOG_HMM_ARM_SAN_R->SANA->TEXTURES
4. Navigate to "Change Custom TFC"
5. Select the "Textures_DLC_CON_AshWar.tfc" as the designated TFC. Select both Marine_00 and Marine_00_Explore in the right toolbar.
6. Change the textures for the Diff, Norm and Spec textures
7. Hit the "Save Changes Button"
8. Hit the "Rebuild Database" button
9. Confirm that thumbnails show new textures in their respective locations
10. Exit texplorer
11. Generate a new TOC, via the AutoTOC feature
12. Boot up the game. Navigate to the CIC and then select a mission
Results
1. In the pre-mission weapon selection and power customization, James' textures reflect their goal
2. Once the mission begins, James reverts back to the vanilla textures. The game completely ignores any new textures that I've applied for it
Pictures:
Pre-Mission power selection

In-mission power selection

In-mission gameplay
Modified Mesh
Steps Involved:
1. Copy and Paste Marine_00 and Marine_00_Explore into a pre-created DLC folder (I utilized the DLC_CON_AshWar folder in this instance)
2. Start up Texplorer and rebuild the tree with only DLC_CON_AshWar selected
3. Navigate to BIOG_HMM_ARM_SAN_R->SANA->TEXTURES
4. Navigate to "Change Custom TFC"
5. Select the "Textures_DLC_CON_AshWar.tfc" as the designated TFC. Select both Marine_00 and Marine_00_Explore in the right toolbar.
6. Change the textures for the Diff, Norm and Spec textures
7. Hit the "Save Changes Button"
8. Hit the "Rebuild Database" button
9. Confirm that thumbnails show new textures in their respective locations
10. Exit texplorer
11. Navigate to Meshplorer. Select Marine_00 pcc in the DLC_CON_AshWar folder
12. Change the mesh for the body, utilizing a UPK file, for all the LODs
13. Save the PCC
14. Repeat Step 11 to 13 for the Marine_00_Explore PCC
15. Generate a new TOC, via the AutoTOC feature
16. Boot up the game. Navigate to the CIC and then select a mission
Results1. In the pre-mission weapon selection and power customization, James' textures amd meshes reflect their goal
2. Once the mission begins, James reverts back to the vanilla textures. The game completely ignores any new textures that I've applied for it. The new mesh is reflected in the game
Pictures
Pre-mission weapon selection

Pre-mission power selection

In-mission power selection
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Conclusions:
There you have it. Its not the meshes that are causing the problems (as the textures are being applied properly...its just for the pre-mission files).
Could texplorer have problems storing 2048 textures in user-created-tfcs for multiple PCCs? Is this a known limit (previous texture modifications were in the 1024 size)