The D.C. Court of Appeals has ruled that emails maintained on private email accounts can still be subject to FOIA - the Washington Post has more on the decision.
This is an evolving issue that arises when government officials do official government business on private emails. The issue has arisen for over the past decade and has spanned multiple presidential administrations.
The way to stop this from happening in the first place is strong Record Management policies including training of ALL agency officials, hopefully on their first day in office. Knowledge of the proper way to retain records, including the use of email, will cause many problems to not occur in the first place as well as increase transparency in the government.