If you update the plugin, the customization changes will be gone automatically, that should resolve that problem.
Import/Export will only work if both the staging and the Production runs the exact same plugin version AND if the production is indeed the exact same copy of the staging (including the database). It's because for example categories and all other terms (and other things as well) can have very different IDs if the database is not exactly the same row-to row. The search options store the excluded category IDs, included term IDs etc.., but if those are different or non-existent on the production, then it's not going to work. There is no way to resolve this unfortunately, because the term ID is the one and only unique field to identify a category or term or any object in wordpress.
If that's the case, I rather recommend mimicing the configuration on the production instead of export/import to avoid object ID collisions, which can cause plugin malfunction.Best,
If you like my products, don't forget to rate them on codecanyon :)