Thank you for your post.
For Android devices, the behaviour you have described (pins being lost when the map is removed) is correct. On iOS devices, if you delete the map, the layer (which contains any placemarks, tracks, etc. created for that map), will be maintained in the Layers tab. We are currently working on our next release (Avenza Maps 3.5) which will have this Layers tab functionality on Android as well, so the risk of losing data if you remove a map will be significantly decreased.
In regards to the symbology related to layers, our latest release, 3.4 and 3.4.1 feature new symbols which users can enjoy. If you are wanting additional colours or symbol options, this can be achieved by creating a KML/KMZ file in Google Earth, assign different colours and pins to placemarks (can be randomly located placemarks), and then import this file into Avenza Maps. Once imported, the symbols imported will be available on other maps and layers (even if you delete the original file).
I’m not sure what you are referring to when you ask “If I use the same color pin for different locations of similar/associated attributes, does each pin afford a different menu of layers and features?” Are you asking if you use the same colour (e.g. red) on different maps or layers, are the attributes you’ve specified the same? If so, the answer is no. The attributes you specify will be specific to the layer you choose, not the symbol.
If you have any other questions, please feel free to contact us using our Support Form at help.avenzamaps.com and we would be happy to help further.