Plan allows for self direction of accounts. Management fees are currently taken out of each individual's account during the year. One partner wishes to reimburse his account for any fees taken out during the plan year. Can this be done if none of the other participants that are self directing do not reimburse their accounts for any fees taken out during the year?

No. Management fees do not fall under settlor responsibility which the plan should not pay anyway. Any 'deposit' to the account should be treated as a contribution which will lead to other problems such as pre-funding, maybe voluntary contribution failing the ACP test (and probably not in document anyway), blowing 415.......

Have the broker bill management fees directly!