How to translate "de-"?
This is one of those cases where the flexibility of English to simply invent words that are intelligible makes the translation job a lot harder. Thus, there's probably no good answer because it will be a case-by-case basis.

Because de- has a plethora of meanings, there will be a plethora of translations. For de- in the sense of "removal," like "de-caffinated," 去 will likely be used (去咖啡因). In the sense of separation or division，like delamination，you might see 分 (分层). 
Because de- is a latin suffix, it shows up more frequently in scientific or technical words that might have their own way to be expressed in Chinese, such as de-emphasize = 淡化.