All great stuff, thanks for taking part. I've updated the modules to include these files.
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I think your solution is just perfect. There's sometimes just no right or wrong way to do something like this. We just work with the tools that we have and try to fit that into what the situation is. The DM always has the option to turn off terrain occluders if they think that they aren't quite what they would expect or how they would view the situation. The central platform in the Bell map is very problematic since it can be viewed from multiple angles and so there will necessarily be multiple ways to create the LOS. I think your solution is just fine.
For vegetation and boulders etc the first question is usually does this block LOS at all? A shrub or patch of rocky ground might count as difficult terrain by that's not the same as blocking LOS. If the terrain feature is of sufficient height then we'd want terrain occluders around it. If the terrain features are close together then we'd probably be happy with a single blocker - but if you are talking about say a forest which covers half a map then I'd be cutting that up into chunks and drawing occluders in sections. There is, again, no really right or wrong answer to this. You kinda just go with what you feel is right and what is in the description. Remember too that if there isn't going to be a lot of combat in the particular area then it may not be worth spending a huge amount of time agonizing over the situation.
I have updated the module to include your files; thanks again for taking part.
Here is my first try at LOS mapping. I'm sure it needs tweaking. I wasn't sure what to do with the (Spoiler) secret tunnels, so left them alone.
Attachment 31435
Loko
Here's the player map (Map: Dungeon_Players) from 'C01 (5E): Alagoran's Gem' adventure by AAW Games.
The 60' incline and drop to the refuse pile caused a minor headache but achieved by using multiple terrain blocks.