One disadvantage i can think of, is that if you have routing protocols such as ospf, eigrp etc, you will have problems forming neighbor relationships, if you have eigrp or ospf neighbors on secondary subnets.
THe routing protocols will advertise the secondaries, they just won't build neighbor adjacencies across the secondaris. I would try and make the secondary the old addresses, and put the new addresses on the primary, so when you pull the secondaries, it won't impact routing as much....
Another disadvantage is the "route through the router between two hosts on the same wire" syndrom. If you have two hosts, say 10.1.1.2 and 10.1.2.2, on the same wire, and you have the router configured as 10.1.1.1, with a secondary of 10.1.2.1, when 10.1.1.2 wants to reach 10.1.2.2, it will actually forward the packet to the router, since the 10.1.2.2 doesn't look like it's on the same segment. The router will switch the packet back out the same interface to the right host--so the traffic between two hosts on the same wire, but in two different subnets, will cross the wire twice.
Beyond these things, there might be issues with HSRP and/or GLBP that you could run in to, and it could make troubleshooting problems more difficult.
If using secondaries is the best way to convert addressing schemes, and in the end, the network is going to be more summarizable, etc, then it's fine to live with them for a while. It's also possible to use them in situations where none of the issues described thus far have any impact.
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