You need to edit the raws of the new game version to use the tiles and colors of your graphics pack.
This example is from the Ironhand tileset
For example, in 34.08:
plant_standard.txt:
The default entry for Maple is:
[PLANT:MAPLE]
[NAME:maple][NAME_PLURAL:maples][ADJ:maple]
[USE_MATERIAL_TEMPLATE:STRUCTURAL:STRUCTURAL_PLANT_TEMPLATE]
[BASIC_MAT:LOCAL_PLANT_MAT:STRUCTURAL]
[AUTUMNCOLOR]
[USE_MATERIAL_TEMPLATE:WOOD:WOOD_TEMPLATE]
[STATE_NAME:ALL_SOLID:maple]
[STATE_ADJ:ALL_SOLID:maple]
[PREFIX:NONE]
Based on Acer spp.
http://www.fpl.fs.fed.us/documnts/TechSheets/HardwoodNA/htmlDocs/acersp1.html
[SOLID_DENSITY:540] Used a more average value. Softer maples are around 400, harder ones around 600.
[STATE_COLOR:ALL_SOLID:RUST]
[TREE:LOCAL_PLANT_MAT:WOOD]
[TREE_TILE:5]
[PREFSTRING:autumn coloration]
[DRY]
[BIOME:FOREST_TEMPERATE_BROADLEAF]
[BIOME:GRASSLAND_TEMPERATE]
[BIOME:SAVANNA_TEMPERATE]
[BIOME:SHRUBLAND_TEMPERATE]
[SAPLING]
The edited entry for Maple is:
[PLANT:MAPLE]
[NAME:maple][NAME_PLURAL:maples][ADJ:maple]
[USE_MATERIAL_TEMPLATE:STRUCTURAL:STRUCTURAL_PLANT_TEMPLATE]
[BASIC_MAT:LOCAL_PLANT_MAT:STRUCTURAL]
[AUTUMNCOLOR]
[USE_MATERIAL_TEMPLATE:WOOD:WOOD_TEMPLATE]
[STATE_NAME:ALL_SOLID:maple]
[STATE_ADJ:ALL_SOLID:maple]
[PREFIX:NONE]
Based on Acer spp.
http://www.fpl.fs.fed.us/documnts/TechSheets/HardwoodNA/htmlDocs/acersp1.html
[SOLID_DENSITY:540] Used a more average value. Softer maples are around 400, harder ones around 600.
[STATE_COLOR:ALL_SOLID:RUST]
[TREE:LOCAL_PLANT_MAT:WOOD]
[TREE_TILE:5] <---------
[TREE_COLOR:6:10:0] <---------
[DEAD_TREE_TILE:160] <---------
[DEAD_TREE_COLOR:7:7:0] <---------
[PREFSTRING:autumn coloration]
[DRY]
[BIOME:FOREST_TEMPERATE_BROADLEAF]
[BIOME:GRASSLAND_TEMPERATE]
[BIOME:SAVANNA_TEMPERATE]
[BIOME:SHRUBLAND_TEMPERATE]
[SAPLING]
You can go through all of the txt files in the raw folder and add and update the tile and color values from the previous graphics version. You can't just copy the while file over the newer one or you will screw up the game. It takes a bit of time, but it will work. Scan through every txt file and compare the files for differences.