UnknownWord1
UnknownWord2
UnknownWord3
UnknownWord1
UnknownWord2
UnknownWord3

ABCDE
ACDBE
EBCDA
ABCDE
ACDBE
EBCDA

private static Random random = new Random();
public static string RandomString(int length = 5)
{
    const string chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZ";
    return new string(Enumerable.Repeat(chars, length)
        .Select(s => s[random.Next(s.Length)]).ToArray());
}

var randoms = lines.GroupBy(x => x).Where(x => x.Count() > 1).ToDictionary(x => x.Key, x => RandomString());

var result = lines.Select(x => randoms.FirstOrDefault(f => f.Key == x).Value ?? x);

import random
chars = 'ABCDEFGHIJKLMNOPQRSTUVWZYZ'
lst = ['Word1', 'Word2','Word3','Word1','Word2']
map = {}
strset = set()
result = []
for line in lst:
    if line in map:
        result.append(map[line])
    else:
        rstr = ''.join([chars[random.randrange(26)] for _ in range(5)])
        while rstr in strset:
            rstr = ''.join([chars[random.randrange(26)] for _ in range(5)])
        map[line] = rstr
        strset.add(rstr)
        result.append(rstr)

print(result)

['SQMHZ', 'VBEZB', 'YNTDZ', 'SQMHZ', 'VBEZB']