Hi Kannan,
What's a Multiprovider? As the name says it can contain several infocubes, ods, virtual providers etc.. In the case of the BWA usually you will have InfoCubes, therefore you will have to reindex each Infocube indexes, and not a Multiprovider. But if you go to t-code RSDDBIAMON you will find the alert with a list of the indexes that need to be reindexed. Now the infocube in the MP is not on BWA and it's showing this alert, this is not possible, unless if once upon a time that infocube was on BWA, then you will have to delete manually these possibles garbage indexes. Please review note 1791048 for more details.
Thanks,
Diego Seben.