1. Are you trying to extract binks to use bpk one them?
And also, the file won't patch back unless all the HEX was copied inside the MAIN file to a new FILE.
I will refer you to
Masquerade's Explanation.
The only change is that, if you want to patch back a file, you must select its HEX using Select Blocks and copy it into a NEW file (create a new file using HxD) and then save it. This way you will have a CRC perfect file and it also patchable.
NOTE : All of the above process must be done within the MAIN file.
Which game are you trying to compress, you can use QUICKBMS, if a script exist since its re-import function is convenient.
Make sure that the file doesn't have any streams because the file size will expand upon this method and re-patching is out of question in such cases, unless you are using QUICKBMS.