Having the same issue myself

cant find the mod in mod options

did a test with just this and the framework and the setting show up like normal, its probably a mod conflict, im gonna see if i can find whats doing it on my end

its EdB prepare carefully
Luckily it looks like if you take that out of your load order you can make changes to the settings, and it will carry over when you put prepare carefully back in

(edit for clarity: Its not JUST prepare carefully, seems like several mods are doing it, that was just the one doing it on my end. More examples would be helpful. Thanks Moose and Dutchman for clearing that up)

Not in my load order gotta be something different for me

Error while instantiating a mod of type VSE.SkillsMod: System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> System.InvalidProgramException: Invalid IL code in (wrapper dynamic-method) MonoMod.Utils.DynamicMethodDefinition:CharacterEditor.SkillTool.GetSkillAsSeparatedString_Patch0 (RimWorld.SkillRecord): IL_0085: call 0x00000021


[Ref A943E644]
at HarmonyLib.PatchFunctions.UpdateWrapper (System.Reflection.MethodBase original, HarmonyLib.PatchInfo patchInfo) [0x00094] in <abec11463bc04855a5322a0a868aeb22>:0
at HarmonyLib.PatchProcessor.Patch () [0x000fc] in <abec11463bc04855a5322a0a868aeb22>:0
at HarmonyLib.Harmony.Patch (System.Reflection.MethodBase original, HarmonyLib.HarmonyMethod prefix, HarmonyLib.HarmonyMethod postfix, HarmonyLib.HarmonyMethod transpiler, HarmonyLib.HarmonyMethod finalizer) [0x0002a] in <abec11463bc04855a5322a0a868aeb22>:0
at VSE.CharacterEditorPatches.Do (HarmonyLib.Harmony harm) [0x0019c] in <01a0c5deb2f94ffeaefc22069c727ab1>:0
at VSE.ModCompat.Init () [0x00096] in <01a0c5deb2f94ffeaefc22069c727ab1>:0
at <0x2509754e160 + 0x00152> <unknown method>
at (wrapper managed-to-native) System.Reflection.MonoCMethod.InternalInvoke(System.Reflection.MonoCMethod,object,object[],System.Exception&)
at System.Reflection.MonoCMethod.InternalInvoke (System.Object obj, System.Object[] parameters) [0x00002] in <eae584ce26bc40229c1b1aa476bfa589>:0
--- End of inner exception stack trace ---
[Ref B296B70D]
at System.Reflection.MonoCMethod.InternalInvoke (System.Object obj, System.Object[] parameters) [0x00014] in <eae584ce26bc40229c1b1aa476bfa589>:0
at System.Reflection.MonoCMethod.DoInvoke (System.Object obj, System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x0007a] in <eae584ce26bc40229c1b1aa476bfa589>:0
at System.Reflection.MonoCMethod.Invoke (System.Reflection.BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00000] in <eae584ce26bc40229c1b1aa476bfa589>:0
at System.RuntimeType.CreateInstanceImpl (System.Reflection.BindingFlags bindingAttr, System.Reflection.Binder binder, System.Object[] args, System.Globalization.CultureInfo culture, System.Object[] activationAttributes, System.Threading.StackCrawlMark& stackMark) [0x00213] in <eae584ce26bc40229c1b1aa476bfa589>:0
at System.Activator.CreateInstance (System.Type type, System.Reflection.BindingFlags bindingAttr, System.Reflection.Binder binder, System.Object[] args, System.Globalization.CultureInfo culture, System.Object[] activationAttributes) [0x00095] in <eae584ce26bc40229c1b1aa476bfa589>:0
at System.Activator.CreateInstance (System.Type type, System.Object[] args) [0x00000] in <eae584ce26bc40229c1b1aa476bfa589>:0
at Verse.LoadedModManager.CreateModClasses () [0x00076] in <957a20e0be784a65bc32cf449445b937>:0
UnityEngine.StackTraceUtility:ExtractStackTrace ()
(wrapper dynamic-method) MonoMod.Utils.DynamicMethodDefinition:Verse.Log.Error_Patch6 (string)
Verse.LoadedModManager:CreateModClasses ()
Verse.LoadedModManager:LoadAllActiveMods (bool)
Verse.PlayDataLoader:DoPlayLoad ()
Verse.PlayDataLoader:LoadAllPlayData (bool)
Verse.Root/<>c:<Start>b__6_1 ()
Verse.LongEventHandler:RunEventFromAnotherThread (System.Action)
Verse.LongEventHandler/<>c:<UpdateCurrentAsynchronousEvent>b__28_0 ()
System.Threading.ThreadHelper:ThreadStart_Context (object)
System.Threading.ExecutionContext:RunInternal (System.Threading.ExecutionContext,System.Threading.ContextCallback,object,bool)
System.Threading.ExecutionContext:Run (System.Threading.ExecutionContext,System.Threading.ContextCallback,object,bool)
System.Threading.ExecutionContext:Run (System.Threading.ExecutionContext,System.Threading.ContextCallback,object)
System.Threading.ThreadHelper:ThreadStart ()

Its definitely not Prepare Carefully, since I dont use that buggy outdated mess and Im having the no settings issue

hmm, no clue where the overlap is then. Maybe several mods are screwing with the same file? Ill put a clarification on my other post.
Can other people try finding what it is in their list? More examples couldn't hurt.

Not sure what changed but its working for me now

In my case, it was because of RandomPlus.

Thanks for the tip, can confirm removal of RandomPlus from my mod list restored the VSE mod options menu.

Character Editor will also cause your settings menu to disappear and throw an exception during load.

seems to be any mod that changes the pawn making stage of game start

Character Editor works fine for me so probably a proper load order will fix that.

For me the mod causing this issue was mad skills, but using mad skills+ fixed the problem for me.