Encrypting device - safe with custom ROM/kernel?

Hey guys, I've been trying to find a simple answer to this but can't so was wondering if someone can help me out!

I decrypted my device very early on. I'm running latest Chroma with elemental X (android 6.0.1) . However I think I'd like me device to be encrypted. Now I know I can do this via security settings... But I was wondering if this will affect me use of TWRP, flashing ROMs, root etc.

Or will everything just work the same?


Thanks in advance!!

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