I'm having a similar issue to this post, except in my attribute template popup, I'm configuring links to open other maps in Collector itself (i.e. arcgis-collector://?itemID=XXXXXXXX) and the map with this attribute template popup is opened in Collector. In other words, I want to open a map in Collector that has layers with attribute templates that open other maps in Collector.
If I long press on one of these links and choose the copy option then paste the link into Safari it successfully opens the new map in collector. I have seen in other posts that Collector now opens all urls in an external browser (Safari) but this does not seem to be true - 10.4.2 still opens them in a Collector browser window. I suspect if it opened them in an external browser, the custom url scheme would work.
Also, if I open the same map in Explorer for ArcGIS and click one of these links, Collector opens the requested web map.