I have two routers R1 and R2 configured with multilink. Everything works fine when both the links are working fine but when one of the link becomes flapping link then ping response also suffers with many RTOs. Then i have to shut down the flapping link for smooth operation. Now Is there any way to fix this without shutting down the interface?
Waiting for your response..
Configure keepalive on both ends. As long as your IOS support, you can use ip SLA, but ip SLA can not bring down the interface by itself.
edit:hightlight can not
MLPPP link fragments all packets and distributes across multiple links; when one side of the member point to pint link is down while the remote side reminds up, the fragmentation and reassembly fails apart. One side keeps sending the fragmented packets through all member links and the remote side cannot reassemble it. That will cause fragmentation errors and packet drops, and this could be the problem you are having.
One solution is you can decrease the interface keepalive; by doing that you can make the remote site quickly notice the MLPPP link is down.