Can a mesh Collider work with an animated skinned Mesh.

From my own experience trying to update a mesh collider frame by frame is terribly slow, instead I found a work around by simply updating the mesh collider when I need it per theANMATOR2b suggestion. I tweaked the script I found here and added it to each game object with a mesh collider I would like to update.

 using UnityEngine;
 using System.Collections;
 
 public class SkinnedCollisionHelper : MonoBehaviour
 {
     // Public variables
     // Instance variables
     private CWeightList[] nodeWeights; // array of node weights (one per node)
     private Vector3[] newVert; // array for the regular update of the collision mesh
     private Mesh mesh; // the dynamically-updated collision mesh
     private MeshCollider collide; // quick pointer to the mesh collider that we're updating
                                   // Function:    Start
                                   //      This basically translates the information about the skinned mesh into
                                   // data that we can internally use to quickly update the collision mesh.
     void Start()
     {
         SkinnedMeshRenderer rend = GetComponent(typeof(SkinnedMeshRenderer)) as SkinnedMeshRenderer;
         collide = GetComponent(typeof(MeshCollider)) as MeshCollider;
         if (collide != null && rend != null)
         {
             Mesh baseMesh = rend.sharedMesh;
             mesh = new Mesh();
             mesh.vertices = baseMesh.vertices;
             mesh.uv = baseMesh.uv;
             mesh.triangles = baseMesh.triangles;
             newVert = new Vector3[baseMesh.vertices.Length];
             short i;
             // Make a CWeightList for each bone in the skinned mesh         
             nodeWeights = new CWeightList[rend.bones.Length];
             for (i = 0; i < rend.bones.Length; i++)
             {
                 nodeWeights[i] = new CWeightList();
                 nodeWeights[i].transform = rend.bones[i];
             }
 
             // Create a bone weight list for each bone, ready for quick calculation during an update...
             Vector3 localPt;
             for (i = 0; i < baseMesh.vertices.Length; i++)
             {
                 BoneWeight bw = baseMesh.boneWeights[i];
                 if (bw.weight0 != 0.0f)
                 {
                     localPt = baseMesh.bindposes[bw.boneIndex0].MultiplyPoint3x4(baseMesh.vertices[i]);
                     nodeWeights[bw.boneIndex0].weights.Add(new CVertexWeight(i, localPt, bw.weight0));
                 }
 
                 if (bw.weight1 != 0.0f)
                 {
                     localPt = baseMesh.bindposes[bw.boneIndex1].MultiplyPoint3x4(baseMesh.vertices[i]);
                     nodeWeights[bw.boneIndex1].weights.Add(new CVertexWeight(i, localPt, bw.weight1));
                 }
 
                 if (bw.weight2 != 0.0f)
                 {
                     localPt = baseMesh.bindposes[bw.boneIndex2].MultiplyPoint3x4(baseMesh.vertices[i]);
                     nodeWeights[bw.boneIndex2].weights.Add(new CVertexWeight(i, localPt, bw.weight2));
                 }
 
                 if (bw.weight3 != 0.0f)
                 {
                     localPt = baseMesh.bindposes[bw.boneIndex3].MultiplyPoint3x4(baseMesh.vertices[i]);
                     nodeWeights[bw.boneIndex3].weights.Add(new CVertexWeight(i, localPt, bw.weight3));
                 }
             }
 
             UpdateCollisionMesh();
         }
         else
         {
             Debug.LogError(gameObject.name + ": SkinnedCollisionHelper: this object either has no SkinnedMeshRenderer or has no MeshCollider!");
         }
     }
 
     // Function:    UpdateCollisionMesh
     //  Manually recalculates the collision mesh of the skinned mesh on this
     // object.
     public void UpdateCollisionMesh()
     {
         if (mesh != null)
         {
             // Start by initializing all vertices to 'empty'
             for (int i = 0; i < newVert.Length; i++)
             {
                 newVert[i] = new Vector3(0, 0, 0);
             }
 
             // Now get the local positions of all weighted indices...
             foreach (CWeightList wList in nodeWeights)
             {
                 foreach (CVertexWeight vw in wList.weights)
                 {
                     newVert[vw.index] += wList.transform.localToWorldMatrix.MultiplyPoint3x4(vw.localPosition) * vw.weight;
                 }
             }
 
             // Now convert each point into local coordinates of this object.
             for (int i = 0; i < newVert.Length; i++)
             {
                 newVert[i] = transform.InverseTransformPoint(newVert[i]);
             }
 
             // Update the mesh (& collider) with the updated vertices
             mesh.vertices = newVert;
             mesh.RecalculateBounds();
             collide.sharedMesh = mesh;
         }
     }
 }
 
 class CVertexWeight
 {
     public int index;
     public Vector3 localPosition;
     public float weight;
     public CVertexWeight(int i, Vector3 p, float w)
     {
         index = i;
         localPosition = p;
         weight = w;
     }
 }
 
 class CWeightList
 {
     public Transform transform;
     public ArrayList weights;
     public CWeightList()
     {
         weights = new ArrayList();
     }
 }

I called the update collision mesh function from another script and implemented it into another function like this

  SkinnedCollisionHelper[] items = FindObjectsOfType<SkinnedCollisionHelper>();
         foreach (SkinnedCollisionHelper item in items)
         {
             item.UpdateCollisionMesh();
         }

I use a play animation, and a pause animation function in my game. I simply add the previous short script into my pause function and whenever in the game I click pause, the mesh updates to fit. This is how I implement that into my Play and Pause Animation script.

 using UnityEngine;
 using System.Collections;
 using System;
 
 public class Play_Pause : MonoBehaviour
 {
     public Animation anim;
     public void Play()
     {
         GetComponent<Animation>().Play();
         anim = GetComponent<Animation>();
         foreach (AnimationState state in anim)
         {
             state.speed = 1F;
         }
     }
 
     public void Pause()
     {
         SkinnedCollisionHelper[] items = FindObjectsOfType<SkinnedCollisionHelper>();
         foreach (SkinnedCollisionHelper item in items)
         {
             item.UpdateCollisionMesh();
         }
 
         anim = GetComponent<Animation>();
         foreach (AnimationState state in anim)
         {
             state.speed = 0F;
         }
     }
 }

This does require you to have a Pause feature in your game. At least for my situation this works great. Hopefully it can be useful for anyone else who may have something similar