Migration from SEPM 12.1.RU2 to 12.1.RU5 issue

Previously when I tried to migrate from SEPM 12.1.RU2 to 12.1.RU5 there isue in which some of the Apache files didn't get replaced as result the apache service was not starting. I logged a case with Symantec they were also not able to solve the issue. So I had to move back to RU2. Did anybody face the same issue? Is there any solution for it?