If I encode a video above source and then later do a final encode, will I lose extra quality vs the final encode directly? I am very happy with my Handbrake settings for my final encodes but I have a video that needs to be edited first. I intend to use Vegas Pro to do this but the default encoding settings create terribly large files. I know I can experiment and find a closer bitrate to my Handbrake settings but I'd like to avoid this for simplicity. Can I still make a final encode with Handbrake without losing quality if I first encode at or above source?

Edit: My question is slightly different, I wanted to know about encoding first to a higher or equal to source bitrate and then re-encoding to a final bitrate. Based on my answer I got, it seems that unless you encode to lossless, some quality will always be lost.
Yes, if you save your video in loseless codec. Unfortunately, this can produce very large files. Also you can try to find frameservers to avoid intermediate files, for frameservers was for older versions of Vegas, I don't know support of this feature in modern versions of Vegas.