IIRC, Indonesia has some weird rules about the specific airline's "name" holding landing rights etc. (as opposed to an airline company holding rights). It proved problematic in the past for Virgin, with (I think) "Virgin Blue" being given rights at DPS, but when they attempted to use a "Pacific Blue" aircraft they met a bureaucratic roadblock, same-same with Valuair at Jetstar, so not surprising that something similar is happening with Skywest now as Virgin Australia.
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