I'd like to add that if it were me, and I really wanted to first do the auto generate of the navmesh before hand working things, I'd search out on the web other people having the same issues with either time length of the generation due to size of the dungeon or potential issues where the generation just would not complete. At least then you might find that either the time length may be potentially a number of hours depending on size, or there may be some error with the dungeon preventing the generation from completing. If it were the time, I'd just let it run for as long as needed.
I'm not saying that the auto generation is necessarily the best way, just saying if it was me, and I wanted a layout to start with, despite the cleanup needed, I'd try to get it to work.
I'm making quest content for a big Lotr world space mod, and I've found a lot of areas look like the creator just did the auto generate navmesh and moved on, surely for the sake of time and due to the scope of what he was trying to accomplish. I've had to clean things up along the way, but ironically only as per needed for the quest content to work as intended in specific areas. So in this case, if the Lotr world mod author had tried to do everything by hand, he may have never completed a number of world areas (including interiors) because of the extra time and work involved, and for my part I don't mind cleaning up areas here and there to get quest content to work while leaving the rest as is.
Just saying, there are pluses and minus's here. Just depends on what is needed really.
Don't forget to backup the .Esp often too, in my quest mod that has been in the works for about 5 months I have 143 backups currently. I backup after I make significant changes/additions, and I backup when I know I'm about to change things that may have the chance of negatively affecting work I have done. I've reverted to numerous backup versions at least 5 times if not more, and it can save a lot of time and avoid frustration. The frequency of how often I personally backup things is probably nearly once per session that I spend time on my mod.
Edited by sornan, 19 November 2020 - 04:30 PM.