I have not tested it personally, but I've been told that if you have 2 epic spell focus feats (eg necro and ench) you can take the same spell specialty feats (necro and ench again), as the only pre-reqs of each is that you have at least one epic spell focus *other* than that specialty (eg necro sees you have ench, and ench sees you have necro).
Just tested, took epic SF necro and conj, then took specialty in both.I will have to see if I have a character that is high enough in levels to repec and try this to verify.
In the meantime I will see if there is some way I can make the system check for this. Otherwise we will just need to turn off the safe guards and people will need to remember they cannot take Necro if Necro is the only Epic Spell Focus they have.