This issue was already reported in 2013, but apparently still not fixed. There’s scripts in the other threads, also, to try to deal with the problem.
Deprecating old IPv6 prefix when removed or replaced RFC6204
http://forum.mikrotik.com/t/deprecating-old-ipv6-prefix-when-removed-or-replaced-rfc6204/66526/1
IPv6 connectivity problems…
http://forum.mikrotik.com/t/ipv6-connectivity-problems/70214/1