Hi,
It is possible to have interface flapping caused by MTU mismatches but only if the receiving port is the one with the lower MTU as this can cause input errors and others, increasing the MTU only increases the interface's capabilities for the traffic's size.
Since you have a 6500 you can change the MTU size on the go, this platform does not require a reload.
Here is a good document about this on different platforms:
http://www.cisco.com/en/US/products/hw/switches/ps700/products_configuration_example09186a008010edab.shtml#c1
I hope it helps
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