Ok. I understand. I'll dig deeper into this issue elsewhere. But I'm grateful for your advice and guidance on what to do next. Good luck! ^ ^

Hello Zappy. If you have time, please help me by telling me exactly what to do with this. I made him a new inner mouth. And this is the result... His ears were also changed and repaired. But this is what happens when I move Shape Keys. When I detailed the ears, the mount was set to Basis. I didn't change any other settings. Why is this happening? >.<;
Link: https://imgur.com/a/EeAnH3D

Oh my god!!! Finally, it really worked! ^ ^ Look at this. With your help, I found the cause of his model's eye problem. THANKS! :D
___
Well.. I wanted to ask you one more thing. Again, I apologize for the inconvenience. I am very curious. My mind rests only when I find the reason for something. Another major issue I would like to mention is his mouth. "Inner mouth". He doesn't have a inner mouth. And I want to ask if it is possible to add an inner mouth to his mouth using Blender program. I'm a beginner at this so I'm lacking in knowledge. ^ ^
Link: https://imgur.com/a/Lpbau1n

Hi Zappy. hmm.. I have tried different changes the codes in his eyes as you suggested. Gladly his eyes returned to normal, but for some reason the eye pupils stopped moving. I have also been searching the internet for a solution to this problem. Any idea?
Link: https://imgur.com/a/G4Rhgny
___
I have sent you the code /.vmt/ which is the root of the problem.
_________________________________________________________
"EyeRefract"
{
"$Iris" "models/silco/iris_dragon"
"$AmbientOcclTexture" "models/silco/eyeball_ao"
"$Envmap" "models/silco/eye-reflection-cubemap-"
"$CorneaTexture" "models/silco/eye-cornea"
"$lightwarptexture" "models/silco/eye_lightwarp"


"$EyeballRadius" "1.10" // Default 0.5
"$AmbientOcclColor" "[0.2 0.2 0.2]" // Default 0.33, 0.33, 0.33
"$Dilation" "0.5" // Default 0.5
"$ParallaxStrength" "0" // Default 0.25
"$CorneaBumpStrength" "0.5" // Default 1.0

"$halflambert" "1"
"$nodecal" "1"

// These effects are only available in ps.2.0b and later

"$ambientocclusion" "1"
"$RaytraceSphere" "0" // Default 1 - Enables raytracing in the pixel shader to make the eyeball look round
"$SphereTexkillCombo" "0" // Default 1 - Enables killing pixels that don't ray-intersect the sphere
}

Oh, It makes sense. His eyes, like before, were too transparent, like marble. But with this change as per your instructions, the eyes look a bit rounder. Hopefully if I tweak his .vmt configuration code a bit more it will fix this bug. But I'm not sure.
Link: https://imgur.com/a/xYBeJ70

Ok. Got it. :) Thank you. ^ ^ You're my hero! This code is working! The Shape Keys are back to normal. Let me show you how it changed. ;) But sadly his eyes could not be fixed. I'm thinking it might be related to his .vmt configuration.
Link: https://imgur.com/a/quemq9T
_______________________________________________________
// Created by Crowbar 0.34.0.0

$ModelName "silco/silco.mdl"
$eyeposition 0 0 70
$attachment "Eyes" "bip_head" 0 -4.49933 79.0266 absolute
$attachment "RightEye" "bip_head" -1.48725 -4.49933 79.0266 absolute
$attachment "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 absolute


$model silco "silco.dmx" {
eyeball "RightEye" "bip_head" -1.48725 -4.49933 79.0266 "eyeball_R" 1 0 "pupil_r" 0.63
eyeball "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 "eyeball_L" 1 0 "pupil_l" 0.63

flexcontroller "Eyes" range -45 45 "Eyes_UpDown"
flexcontroller "Eyes" range -45 45 "Eyes_RightLeft"

}

$MostlyOpaque

$CDMaterials "models\silco\"

$Sequence "idle" {
"silco.dmx"
fadein 0.2
fadeout 0.2
fps 30
}

~Shape keys problem... Even after changing it to this, it didn't work "QC code options". I'm very confused it. >.<
________________________________________________________
// Created by Crowbar 0.34.0.0

$ModelName "silco/silco.mdl"
$eyeposition 0 0 70
$attachment "Eyes" "bip_head" 0 -4.49933 79.0266 absolute
$attachment "RightEye" "bip_head" -1.48725 -4.49933 79.0266 absolute
$attachment "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 absolute


$model silco "silco.dmx" {
eyeball "RightEye" "bip_head" -1.48725 -4.49933 79.0266 "eyeball_R" 1 0 "NotUsed" 1
eyeball "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 "eyeball_L" 1 0 "NotUsed" 1

flexcontroller "Eyes" range -90 90 "Eyes_UpDown"
flexcontroller "Eyes" range -90 90 "Eyes_RightLeft"

}

$Body "silco" "silco.dmx"

$SurfaceProp "flesh"

$Contents "solid"

$MaxEyeDeflection 90

$MostlyOpaque

$CDMaterials "models\silco\"

$CBox 0 0 0 0 0 0

$BBox -8.749 -18.9 -0.164 5.622 18.576 74.046


$Sequence "idle" {
"silco.dmx"
fadein 0.2
fadeout 0.2
fps 30
}

$CollisionModel "silco.dmx"
{
$mass 100
$inertia 1
$damping 0
$rotdamping 0
$concave

}

I have sent you the code for his eye setup. I thought another model's eye setup would match his eyes, but this happened. Which of these should I fix? Please help me. >.<
___________________________________________________________
"EyeRefract"
{
"$Iris" "models/silco/iris_azure"
"$AmbientOcclTexture" "models/silco/eyeball_ao"
"$Envmap" "models/silco/eye-reflection-cubemap-"
"$CorneaTexture" "models/silco/eye-cornea"
"$lightwarptexture" "models/silco/eye_lightwarp"


"$EyeballRadius" "1.02" // Default 0.5
"$AmbientOcclColor" "[0.2 0.2 0.2]" // Default 0.33, 0.33, 0.33
"$Dilation" "0.65" // Default 0.5
"$ParallaxStrength" "0.25" // Default 0.25
"$CorneaBumpStrength" "1.3" // Default 1.0

"$halflambert" "1"
"$nodecal" "1"

// These effects are only available in ps.2.0b and later

"$ambientocclusion" "1"
"$RaytraceSphere" "1" // Default 1 - Enables raytracing in the pixel shader to make the eyeball look round
"$SphereTexkillCombo" "1" // Default 1 - Enables killing pixels that don't ray-intersect the sphere
}

This was the result when I adjusted his eyes. And the Shape keys problem.
Link: https://imgur.com/a/M3wkr97

Oh, sorry to bothering to you. I just successfully adjusted his eyes. But there was another problem here. >.< Just when I thought I had made the model all right, the Shape keys stopped working again. What did I miss?! Please check this QC code.
___________________________________________________________
// Created by Crowbar 0.34.0.0

$ModelName "silco/silco.mdl"
$eyeposition 0 0 70
$attachment "Eyes" "bip_head" 0 -4.49933 79.0266 absolute
$attachment "RightEye" "bip_head" -1.48725 -4.49933 79.0266 absolute
$attachment "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 absolute

$BodyGroup "silco"
{
studio "silco.dmx"
}

$model silco "silco.dmx" {
eyeball "RightEye" "bip_head" -1.48725 -4.49933 79.0266 "eyeball_R" 1 0 "NotUsed" 1
eyeball "LeftEye" "bip_head" 1.48725 -4.49933 79.0266 "eyeball_L" 1 0 "NotUsed" 1

flexcontroller "Eyes" range -90 90 "Eyes_UpDown"
flexcontroller "Eyes" range -90 90 "Eyes_RightLeft"

}

$SurfaceProp "flesh"

$Contents "solid"

$MaxEyeDeflection 90

$MostlyOpaque

$CDMaterials "models\silco\"

$CBox 0 0 0 0 0 0

$BBox -8.749 -18.9 -0.164 5.622 18.576 74.046


$Sequence "idle" {
"silco.dmx"
fadein 0.2
fadeout 0.2
fps 30
}

$CollisionModel "silco.dmx"
{
$mass 100
$inertia 1
$damping 0
$rotdamping 0
$concave

}