Okay. The lesson I learn from this is never use suitebundler to migrate from sandbox to production

@Azi Have you looked to see if you can "dissolve" the bundle? This may only apply in the account the bundle was installed to using the suitebundler process and not when the bundle is copied back across to Sbox but you could check that. At least then you won't have the bundle referenced in SB. If not, then maybe you need to look at dissolving the bundle in Prod before the refresh happens in future.