From Law 2:
"Additional balls which meet the requirements of Law 2 may be placed around the field of play and their use is under the referee’s control"
http://www.thefa.com/football-rules-governance/lawsandrules/laws/football-11-11/law-2---the-ball
I can't see any change in the Law since the days when I was refereeing football (when teams had dinosaurs and pterodactyls for mascots). In local matches in Sheffield parks, where it could take ages to chase after a ball which had run down a steep slope, I remember checking the condition of several balls before each match in order that play could quickly resume while someone trudged down the hill. I also remember helping the ref check several balls before a match at Hillsborough, where I was running a line, so that any ball which disappeared into a stand could quickly be substituted.
As long as the ref is happy with the condition of a replacement ball (having checked it prior to the game or having delegated the task to an assistant referee), I can't see why their should be any problem with replacing it during any stoppage in play.