Multiple video encoding loss
If you must encode at each step, use a lossless codec, or at least at a high bit rate and bit depth. But it's unusual and inefficient to perform intermediate encodings. A decent NLE will let you apply the needed transforms on separate segments or layers and only encode as a final step. 

And note that rendering doesn't imply encoding in the final format. It may mean only performing some actions in the internal NLE format. If your layers can't be played out for preview because of hardware limitations, a render may permit that. But it doesn't commit you. You would still encode using the original elements in a final render.