Could a crypto system that uses non-FIPS crypto but then upgrades complete to FIPS be FIPS certified?
Yes, a device that is FIPS certified need not be restricted to using only FIPS-approved algorithms.  For example, in your case, FIPS has no problems with you supporting Curve25519, as long as the user can turn it off.  That is, the device will need to be able to be set in a mode that it performs only FIPS approved algorithms (and the FIPS approval documentation will have to explain precisely how to do that).

You specifically asked about 'crypto system'; if you're asking about a protocol, a protocol is not FIPS approved; FIPS approved devices, not protocols.