This file is generated internally by the 3DS operating system. It lives in the console’s system memory and NAND storage. When you perform a system transfer or backup, the enctitlekeys.bin file moves along with your other licensed data.
If you are modifying a 3DS or configuring an emulator today, the relevance of encTitleKeys.bin has significantly shifted due to platform updates and architectural changes. The 2018 CDN Change
Which (e.g., GodMode9, Citra) are you trying to configure?