Is this an Ad Hoc or are you using plots and what not too? Since you are using 2 incompatible mods I can see there might be issues. Since you used Scrap Everything the most broken mod you could possibly ever use, did you also make and add the 2 scrap profiles that you will need to your esl for your plan to work in the new game?
I haven't used any SS2 plots yet. I have built the entire settlement and all the foundations (e.g. 2x2 foundation blocks) where to place the plots; all I need to do is to lay down the plots to start my settlement. But what I have built is very detailed and took me some time, which is why I want to properly export this settlement.
Is there any other scrapping mod that SS2 supports other than Scrap Everything? Or should I use vanilla scrapping?
As for Scrap Profiles, I don't know how to create scrap profiles as I am fairly new to modding. I simply exported my settlement twice: once with Scrap Profiles turned ON from the WSWF Mod Config, another time with Scrap Profiles turned OFF from the WSWF Mod Config. Using the WSWF webtool, I created separate ESL files for each of these log exports. Only the one with the Scrap Profile turned OFF is recognized by the game. The ESL with the one which I exported with Scrap Profile turned ON would return something like "This settlement has no saved layouts available" when I try to import a layout from that ESL.
EDIT: Just in case, I'll attach the log file to this post.
In the first place, I want to export my settlement and start over because I started my new game with these quest mods on for the first time: Outcasts & Remnants, Project Valkyrie, 50 Ways to Die at Dr. Nick's, Fusion City Rising, Depravity, Welcome to Goodneighbor, Commonwealth Responders, Subversion, Old Time Religion, and the Machine & Her. In the SS2 Known Issues, it is mentioned that SS2 should not be played with some of these mods on. Hence, if the exporting is not possible, I would like to know if there is a way to properly continue SS2 with these mods on; for example, if I finish Fallout 4 without taking part in those quests. Then I would be able to continue this save file and not export the settlement.