Hulkenberg left Force India to drive for Sauber from the start of this season.
"The idea of the Nico/Paul partnership not continuing into 2013 wasn't our plan," Fernley told Autosport.
"Obviously it slightly de-railed our programme."
Force India has yet to announce a second driver to partner Paul di Resta, with Fernley admitting that the plan had been to keep Jules Bianchi as reserve driver for two years.
"If we'd had an ideal world we'd have liked to run Jules for two years as a third driver."
"Is Jules ready to go into a primary seat? Yes, he is. Absolutely. But we've just got to make sure we tick all the boxes now."