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I have a site that's spread across two domains. Let's say the two sites are example.com and exampledatabase.com.

Right now, when someone leaves example.com to go to exampledatabase.com, it's counted as a bounce.

Is the correct way to remedy this to create a filter and exclude->traffic to hostname->exampledatabase.com?

I don't want this solution to cause unanticipated manipulation of the data within the view.

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As far as I know, Google Analytics filters will let you include or exclude traffic coming to your site, not traffic going away.
Using exclude -> traffic to hostname -> exampledatabase.com will not work, except if you're using the same Google Analytics property id on both sites. Judging by your question that's not the case, they are tracking on their own property id. So, exampledatabase.com will never show up in example.com's Analytics data.

If you want to "tweak" Google Analytics for decreasing your bounce rate when visitors navigate from example.com to databaseexample.com then: Use events: They reduce bounce rate, do not inflate page views.
Use virtual page views: They reduce bounce rate, inflate page views.

Events: Fire an event when your visitors click an URL pointing to databaseexample.com. Read Track outbound links. @GeorgeAnt was on the right track, except for the value for parameter opt_noninteraction, he said set to true, it should be on its default value false.

GeorgeAnt's linked reference (same I included):

By default, the event hit sent by _trackEvent() is considered an interaction hit, which means that it is included in bounce rate calculations. However, when this value is set to true, the type of event hit is not considered an interaction hit.

Track Virtual page views: Fire code when your visitors click an url pointing to Site B, and set a virtual URL, something like /outgoing/url-gone-to-site-b.

You could also track traffic from both domains into one property id, maybe that's what you're looking for, here is the documentation.

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You can use _trackEvent() function for that. Just set the value to true.

You can find more here : Event Tracking

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Should opt_noninteraction be set to true to count as interaction? I guess it's the opposite. – Binarysurf Jul 7 '14 at 17:03

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