These mod files are working for me.
I took your files, and edited the COVERAGE to unique values:
[ID:test]
[NUMERIC_VERSION:1]
[DISPLAYED_VERSION:1]
[EARLIEST_COMPATIBLE_NUMERIC_VERSION:1]
[EARLIEST_COMPATIBLE_DISPLAYED_VERSION:1]
[AUTHOR:DWARFFRAWD]
[NAME:test]
[DESCRIPTION:Problem clearing and recreating with CUT_ITEM command?]
item_armor
[OBJECT:ITEM]
[CUT_ITEM:ITEM_ARMOR_BREASTPLATE]
[ITEM_ARMOR:ITEM_ARMOR_BREASTPLATE]
[NAME:breastplate:breastplates]
[ARMORLEVEL:3]
[UBSTEP:0]
[LBSTEP:0]
[SHAPED]
[LAYER:ARMOR]
[COVERAGE:99]
[LAYER_SIZE:20]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:9]
[HARD]
[METAL]
[CUT_ITEM:ITEM_ARMOR_MAIL_SHIRT]
[ITEM_ARMOR:ITEM_ARMOR_MAIL_SHIRT]
[NAME:mail shirt:mail shirts]
[ARMORLEVEL:2]
[UBSTEP:1]
[LBSTEP:1]
[LAYER:OVER]
[COVERAGE:98]
[LAYER_SIZE:15]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:6]
[HARD]
[METAL]
[STRUCTURAL_ELASTICITY_CHAIN_ALL]
[CUT_ITEM:ITEM_ARMOR_LEATHER]
[ITEM_ARMOR:ITEM_ARMOR_LEATHER]
[NAME:armor:armor]
[PREPLURAL:suits of]
[MATERIAL_PLACEHOLDER:leather]
[ARMORLEVEL:1]
[UBSTEP:1]
[LBSTEP:1]
[SHAPED]
[LAYER:ARMOR]
[COVERAGE:97]
[LAYER_SIZE:20]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:6]
[LEATHER]
[CUT_ITEM:ITEM_ARMOR_COAT]
[ITEM_ARMOR:ITEM_ARMOR_COAT]
[NAME:coat:coats]
[UBSTEP:MAX]
[LBSTEP:1]
[LAYER:COVER]
[COVERAGE:96]
[LAYER_SIZE:20]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:5]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_SHIRT]
[ITEM_ARMOR:ITEM_ARMOR_SHIRT]
[NAME:shirt:shirts]
[UBSTEP:MAX]
[LBSTEP:0]
[LAYER:UNDER]
[COVERAGE:95]
[LAYER_SIZE:10]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:3]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_CLOAK]
[ITEM_ARMOR:ITEM_ARMOR_CLOAK]
[NAME:cloak:cloaks]
[UBSTEP:MAX]
[LBSTEP:1]
[LAYER:COVER]
[COVERAGE:94]
[LAYER_SIZE:15]
[LAYER_PERMIT:150]
[MATERIAL_SIZE:5]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_TUNIC]
[ITEM_ARMOR:ITEM_ARMOR_TUNIC]
[NAME:tunic:tunics]
[UBSTEP:0]
[LBSTEP:1]
[LAYER:UNDER]
[COVERAGE:93]
[LAYER_SIZE:10]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:3]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_TOGA]
[ITEM_ARMOR:ITEM_ARMOR_TOGA]
[NAME:toga:togas]
[UBSTEP:1]
[LBSTEP:1]
[LAYER:OVER]
[COVERAGE:92]
[LAYER_SIZE:30]
[LAYER_PERMIT:100]
[MATERIAL_SIZE:5]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_CAPE]
[ITEM_ARMOR:ITEM_ARMOR_CAPE]
[NAME:cape:capes]
[UBSTEP:0]
[LBSTEP:0]
[LAYER:COVER]
[COVERAGE:91]
[LAYER_SIZE:10]
[LAYER_PERMIT:300]
[MATERIAL_SIZE:3]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_VEST]
[ITEM_ARMOR:ITEM_ARMOR_VEST]
[NAME:vest:vests]
[UBSTEP:0]
[LBSTEP:0]
[LAYER:OVER]
[COVERAGE:90]
[LAYER_SIZE:10]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:2]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_DRESS]
[ITEM_ARMOR:ITEM_ARMOR_DRESS]
[NAME:dress:dresses]
[UBSTEP:MAX]
[LBSTEP:MAX]
[LAYER:UNDER]
[COVERAGE:89]
[LAYER_SIZE:10]
[LAYER_PERMIT:50]
[MATERIAL_SIZE:5]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_ARMOR_ROBE]
[ITEM_ARMOR:ITEM_ARMOR_ROBE]
[NAME:robe:robes]
[UBSTEP:MAX]
[LBSTEP:MAX]
[LAYER:COVER]
[COVERAGE:88]
[LAYER_SIZE:20]
[LAYER_PERMIT:100]
[MATERIAL_SIZE:6]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
item_shoes
[OBJECT:ITEM]
[CUT_ITEM:ITEM_SHOES_SHOES]
[ITEM_SHOES:ITEM_SHOES_SHOES]
[NAME:shoe:shoes]
[LAYER:OVER]
[COVERAGE:99]
[LAYER_SIZE:20]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:1]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[SHAPED]
[CUT_ITEM:ITEM_SHOES_BOOTS]
[ITEM_SHOES:ITEM_SHOES_BOOTS]
[NAME:high boot:high boots]
[ARMORLEVEL:1]
[UPSTEP:1]
[METAL_ARMOR_LEVELS]
[LAYER:OVER]
[COVERAGE:98]
[LAYER_SIZE:25]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:2]
[METAL]
[LEATHER]
[HARD]
[SHAPED]
[CUT_ITEM:ITEM_SHOES_BOOTS_LOW]
[ITEM_SHOES:ITEM_SHOES_BOOTS_LOW]
[NAME:low boot:low boots]
[ARMORLEVEL:1]
[METAL_ARMOR_LEVELS]
[LAYER:OVER]
[COVERAGE:97]
[LAYER_SIZE:25]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:1]
[METAL]
[LEATHER]
[HARD]
[SHAPED]
[CUT_ITEM:ITEM_SHOES_SANDAL]
[ITEM_SHOES:ITEM_SHOES_SANDAL]
[NAME:sandal:sandals]
[LAYER:OVER]
[COVERAGE:96]
[LAYER_SIZE:25]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:1]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[SHAPED]
[CUT_ITEM:ITEM_SHOES_CHAUSSE]
[ITEM_SHOES:ITEM_SHOES_CHAUSSE]
[NAME:chausse:chausses]
[UPSTEP:MAX]
[LAYER:UNDER]
[COVERAGE:95]
[LAYER_SIZE:10]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:3]
[SOFT]
[LEATHER]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
[CUT_ITEM:ITEM_SHOES_SOCKS]
[ITEM_SHOES:ITEM_SHOES_SOCKS]
[NAME:sock:socks]
[LAYER:UNDER]
[COVERAGE:94]
[LAYER_SIZE:10]
[LAYER_PERMIT:15]
[MATERIAL_SIZE:1]
[SOFT]
[STRUCTURAL_ELASTICITY_WOVEN_THREAD]
I then generated a new pocket 5-year world with only the test mod, and verified with DFHack that the objects were being cut and recreated:
[DFHack]# :lua for _,v in ipairs(df.global.world.raws.itemdefs.armor) do print(v.id,v.props.coverage);end
ITEM_ARMOR_BREASTPLATE 99
ITEM_ARMOR_MAIL_SHIRT 98
ITEM_ARMOR_LEATHER 97
ITEM_ARMOR_COAT 96
ITEM_ARMOR_SHIRT 95
ITEM_ARMOR_CLOAK 94
ITEM_ARMOR_TUNIC 93
ITEM_ARMOR_TOGA 92
ITEM_ARMOR_CAPE 91
ITEM_ARMOR_VEST 90
ITEM_ARMOR_DRESS 89
ITEM_ARMOR_ROBE 88
HF60 EI1AAR1 100
HF60 EI1CAR1 50
[DFHack]# :lua for _,v in ipairs(df.global.world.raws.itemdefs.shoes) do print(v.id,v.props.coverage);end
ITEM_SHOES_SHOES 99
ITEM_SHOES_BOOTS 98
ITEM_SHOES_BOOTS_LOW 97
ITEM_SHOES_SANDAL 96
ITEM_SHOES_CHAUSSE 95
ITEM_SHOES_SOCKS 94
HF60 EI1ASH1 100
HF60 EI1CSH1 100
I guess, verify the subdirectory and file names. Mine were:
C:\Games\Dwarf Fortress\playing50\mods\test\info.txt
C:\Games\Dwarf Fortress\playing50\mods\test\objects\item_armor.txt
C:\Games\Dwarf Fortress\playing50\mods\test\objects\item_shoes.txt
Note that it's 'objects', not 'object'. That's tripped me up more that once.
Also note that the files MUST be named 'item_armor.txt' and 'item_shoes.txt'. To be specific, each filename must match the first line of the file, without the .txt extension.
Finally, delete the errorlog.txt file in the Dwarf Fortress directory, generate a new world using your mod, and check if there's anything new in errorlog.txt.