On my file that has both the Crystal Goo and Janeria upgrade, selecting the [Repair] option in Nova's menu can have different effects depending on whether nor not Nova is equipped. If Nova is currently equipped when selecting the [repair] option, then the "Grey Goo Armor" has its numerical stats correctly applied if they are incorrect. However, if Nova is not equipped, then the "Grey Goo Armor" has its numerical stats reset to default. Interestingly, the "Mirrored" flag is still kept by the armor.
This is after using repair with the armor not equipped
This is after using repair with the armor equipped.
This is after using repair with the armor not equipped
This is after using repair with the armor equipped.