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Can we have site collections with different FBA membership providers in same web application. If yes, how will be the entries in config files of CA and STS?

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Authentication is configured at web App level. So you cant have the mix membership in single WEBAPP and single FBA. If you want authenticate against different membership then use different zone for web app.

also have look on it. https://social.msdn.microsoft.com/Forums/en-US/8a174942-22d1-4559-aa5f-d133c1e20fee/fba-with-multiple-membership-providers?forum=sharepointdevelopmentprevious

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