First of all, thank you very much for MAST, this add-on is excellent. 

I would like to make it my main level editor however i'm running into a problem: I'm unable to update(replace) the meshes that I imported in MAST. 

I tried pretty much everything I could, ending up getting these errors, rendering me unable to proceed on the prefab creation tool:

- NullReferenceException: Object reference not set to an instance of an object

- MissingReferenceException: The object of type 'Material" has been destroyed but your are still trying to access it.

It seems that MAST is detecting and trying to add the previously created prefabs, present in subfolders, causing conflict. Is that it ?

Sometimes however it worked, more or less: the level I build kept the prefabs in the hierarchy window, but does not display any meshes in the unity editor. 

And in the worst case, I'm getting lots of meshes stacked at the same place once done importing.

I have no idea what's going on or what I'm doing wrong. Is there a proper way to do so ?

MAST doesn't exactly import meshes, unless you're referring to the tool that creates prefabs out of your models.  There are some known bugs with that tool, but you can create your own prefabs without it.  Also, if you started trying to create prefabs and received an error, you need to delete the materials folder it created before trying again. 

If you're not using MAST's prefab creator and still getting errors, then I recommended deleting all files in FSP\MAST and reinstall MAST from scratch.  I made some naming changes to classes over different versions and old with new files together, you can get errors.

If you need further help, you can reach out to me on Discord:. https://discord.gg/eMKJ5U5

Good luck!

Keith at FSP

Great! In fact I was using MAST prefab creator tool the whole time, it doesn't even crossed my mind to try whitout. I'm going to experiment again and move on discord yes. Thanks for the help!