Assuming the source of the new certificate is the one you're pinning, and the pinning certificate hasn't been revoked, you're probably OK. At some level, you have to trust the system (EDIT: I mean you have to trust that public key crypto works in general, not that the PKI/CA system in particular is trustworthy), and you're already doing everything you reasonably can to verify the server.
Now, with that said, standard practice is to pin only the public key information (which means you can do things like re-issue the same certificate with a new expiration date, without breaking your pinning) and to pin both the key of your current certificate, and a backup key. The backup key is for if you need to rotate or revoke your current certificate, rather than just re-issuing it. The backup key pair can be created in advance, and then you throw the only copy of the backup private key in a vault or something until you need it.
Between the ability to re-issue certificates so long as you don't change the public key, and having a backup key if you do need to change keys, you should have a large window between when you need to rotate/revoke a key, and when the pinning breaks. During this window, you can release an app update that turns the old backup into the primary key, adds a new backup, and removes the no-longer-trusted primary entirely. If necessary, your app can including a version check function that reminds users to upgrade from the store when the keys change.