We faced such an issue with availability of URLs in notification emails generated from BC in most of e-mail clients.
Those URLs which are generated by BC can refer different types of BC clients (web, windows, mobile). This actually gives similar URLs but with different protocols in the beginning. If we use URL for web client (which starts from https://) that works. However, if we want to use URL for different client, lets say, mobile (which starts from ms-dynamicsnav://) this will not work as needed - email clients remove the link leaving only simple text in the message. I can see the link is there if I open the e-mail in desktop version of Outlook. But the same is not possible neither in web version of Outlook or mobile app nor Gmail web or Android app (or other web-based mail service). URL itself is correct and if I open it from different place it starts application as needed.
So the issue is specifically with blocking of URLs by mail clients, probably due to certain security reasons.
Does anyone have any thoughs on how to make those available? Is there any setup possible (put any exceptions or anything like that) for either email clients/apps or in the system? Primary looking for a solution for mobile.