I start with the landclass.xml file. That tells me which scenery textures are used for each landclass, eg "dry woody scrub". It also tells you which .lso and .mos files attach to which .dds textures. (The .dds textures are named the same as the .mos and .lso files) If you have scenery textures floating around that are not listed in the landclass.xml, they are redundant in terms of scenery, except where the textures are required for facilities. You can easily test that by backing up and removing redundant textures from your Assets folder.
When porting over .dds textures to the Assets folder, you need to ensure that you port over the matching .lso file (as specified in the landclass.xml file), and you also need to ensure there are no duplicates in the Asset folder. I always use the same set of sub-folder names in the Assets folder for quick comparison between installs.
<LandClass Id="51" Name="Dry Woody Scrub" Dim="9216" Priority="20" IsWater="No" Mask="GenericLandClassMask.xml">
<Seasons>
<Season Name="Summer">
<Variations>
<Variation Mosaic="051summer1.mos" Scenery="051summer1.lso" />
<Variation Mosaic="051summer2.mos" Scenery="051summer2.lso" />
<Variation Mosaic="051summer3.mos" Scenery="051summer3.lso" />
</Variations>
</Season>
<Season Name="Winter">
<Variations>
<Variation Mosaic="051winter1.mos" Scenery="051summer1.lso" />
<Variation Mosaic="051winter2.mos" Scenery="051summer2.lso" />
<Variation Mosaic="051winter3.mos" Scenery="051summer3.lso" />
</Variations>
</Season>