Login security and plaintext of a password stored in Argon2i to derive a key via halite safe?
1. Is this form of double authentication even helping security?


Possibly, but in general, asking users to remember two passphrases is asking too much. It is less likely that either one of them will be secure enough to be used as password.


  2. Is using the second passphrase to derive the key safe?


Probably, but sharing a password among all the other employees is certainly not secure.

Besides that, using both Argon2i and scrypt on the same input material only slows down your service, while an adversary only needs to perform the fastest one (from their perspective).

If a key is derived after verification of the password then a Key Based KDF such as HKDF can be used.


  3.  ... is this possible without re-encrypting all of the data using the new derived key?


No, for that you'd need a data key as you're describing.




  If that works would Halites Symmetric::encrypt be secure enough for the second key?


Sorry, but that's off topic here; we cannot vouch for the security of a crypto system or library. You can of course do worse than libsodium to encrypt data, but if it is secure also depends on system and implementation details.