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Brushes Delete Themselves if I Edit

TLDR;
I have 288 BSP brushes. If I edit the map ten disappear. Help Please.

I am new to the level editor. I have been using BSP brushes in the level editor to block out a level idea. Once I got to 288 brushes and hit build all was good. Afterward I moved an item and noticed the that the last ten brushes I had placed were removed. I am in need of help as this clearly limits my project. Thank you for you time.