The black circle icon showing where your sub is and which appears on zoomed out levels, and the actual sub shaped icon which appears at close zoomed in levels, are actually small bitmap graphic files, with a .dds extension. Similar files are the squares for map merchant contacts, diamonds, triangles etc.
What the Real Navigation mod does is it replaces all these bitmap files with blank versions, so that nothing appears on the TAI screen or chart. If you want JUST the sub icons back you can add the original files back in yourself in a small custom mod, which you would load after the Real Navigation mod, which would in effect restore these icons back to default and you would be able to see your sub again, but not see map contacts or anything else which Real Nav disables.
I could tell you which files you need to restore but as Berbster says this does kind of negate what Real Nav is about. However, if you are happy to just see where your sub is, for your own enjoyment of the game then let me know and I'll list them. Then its up to you to create the custom mod yourself, which is actually very easy once you have the original versions of these bitmaps.
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