I'm facing an issue when we enable a second IDP (add Claims Provider Trust), then we are not able to navigate between apps without stopping in the HRD (Home Realm Discovery) page. Is there a way to control this?
Depends on the version of AD FS used and your scenario.
You can prevent HRD on the intranet if you are sure they wont need to pick another IDP via HRD. This way users accessing AD FS via a WAP (i.e. on extranet) do HRD but not those accessing AD FS direct (i.e. on intranet)
You can also configure certain relying parties to be associated with specific IDPs. Therefore, if a relying party were associated with just one IDP, the user wont get the choice to do HRD anyway.