Don't worry about it- you're going to see funky behavior with secondary ip addresses.
Traceroute works by sending out ICMP packets with short TTLs. When a router gets a packet with a TTL that it expires, it sends back a packet with its IP address and a "time exceeded message". The IP address a router uses to send back this message is the primary address of the interface, not necessarily the virtual IP address that you sent the packet to.
One thing to keep in mind with secondary IP addressing is that DHCP and IP helper statements aren't going to work for the network of the secondary address- for the same reason I mentioned before. The router can't determine which network you wanted to source that DHCP from- so it sends the DHCP request to the server sourced from the primary address of th interface, not the secondary.
if you're truly migrating off the address space, it's probably a good thing to delete the secondary address, delete the primary address, install the new address as a primary, and the old address as a secondary.