Dictionary<int,string> DictA=new Dictionary<int,string>();
DictA.Add(1,"A");
DictA.Add(2,"B");
DictA.Add(3,"C");
DictA.Add(4,"D");
Dictionary<string,string> DictB=new Dictionary<string,string>();
DictB.Add("A","A1");
DictB.Add("C","C1");
DictB.Add("D","D1");

DictA
.Select(x => new KeyValuePair<int,string>(x.Key,
                                          DictB.ContainsKey(x.Value)
                                          ? DictB[x.Value]
                                          : x.Value)
.ToDictionary(x => x.Key, x => x.Value);

var result = DictA.ToDictionary(a => a.Key, a => DictB.ContainsKey(a.Value) ? DictB[a.Value] : a.Value);

foreach (var item in result)
{
    Console.WriteLine(item.Key + ", " + item.Value);
}

var result =
    DictA
        .ToDictionary(
            a => a.Key,
            a => DictB.ContainsKey(a.Value)
                ? DictB[a.Value]
                : a.Value);

DictA.ToList().ForEach(kv =>
{
    if (DictB.ContainsKey(kv.Value))
        DictA[kv.Key] = DictB[kv.Value];
});