Hi Dan.
Yes, what you have discovered is something many of us have in one way or another.
Myself found this out, going back around 2 years ago. After talking to Lee, and some other users. I was able to build a game with 18 levels, using a build game system, that takes time, yet proves handy in the long for any additional changes or build errors with media (such as weapon textures missing)
Now lets break it down.
You removed some levels and was able to build smaller sections of the game. And very wise to test if a level had an issue.
The running programs in background is fine to consider, however the memory cap will come into play based on level file size.
I will add an example below for others to understand.
I spent many years looking into factors of how errors occur and the below link is the best advice I have for you to compile the game in 1 build without having to update. As Lee informed may/may not occur additional problems.
Also, if you dont want to go with my link, xplosys idea of episodes is a good option. And Deathcow's advice I would follow if this has been able to be expanded on and lifted.
Example. - Including say lightmaps,menus etc etc.
Lvl 1 - 250mb
Lvl 2 - 800mb
Lvl 3 - 500mb
Lvl 4 - 800mb
Lvl 1,2,3 = 1550mb builds. Add level 4 errors out.
Lvl 1,2,4 = 1850mb builds. etc etc.
If you have 10 Lvls say and all sit around 500mb. I suggest break the sections in 3lvls (maybe 4) per part and use my link and build it into 1 using text edits.
All the best.
http://forum.thegamecreators.com/?m=forum_view&t=170920&b=21
This is purely a suggestion, and if you or someone can find another way thats easier, go for it. The above link worked well for me and after bug testing, gave me the option where I could edit 1 lvl, and drop it back into the final build, without having to compile the whole game each time..