For anyone reading this, the Upgrades Plugins don’t currently support checking enums and structs for upgrade safety, see: https://docs.openzeppelin.com/upgrades-plugins/1.x/faq#why-cant-i-use-custom-types
Update: The latest version of the Upgrades Plugins supports checking structs and enums automatically, so you won’t run into this error anymore. See the full announcement at Upgrades with Peace of Mind: "Structs" Edition.
For checking for upgrade safety I suggest writing higher level tests that check all the state before and after an upgrade, see the proxy tests for an example: OpenZeppelin Upgrades: Step by Step Tutorial for Truffle
How are you using your structs? (e.g. in a mapping or a state variable)
Are you able to share your smart contract?
Depending on how you are using your structs, this may limit what changes you can make to state variables in upgrades.