Mostly, what Elva said.
1. Inquisitors vs. Governors? entirely normal.
2. Governors vs. inquisitors? Less likely, because whilst removing governors is unlikely to be a problem for inquisitors beyond a few funny looks, even the mysterious dissappearance of the inquisitor could bring wrath down on the governor. But if he's desperate / ambitious enough, sure. Especially if he's used to being absolute in his own power.
3. If a planet is fairly sparsely populated, as many imperial worlds seem to be, a small force of chaos rebels could well survive for some time. Maybe they're just not big enough to divert a guard regiment to deal with? Maybe the governor is a nimby about military interventions?
4. If there's a serious threat of a chaos incursion even distrustful inquisitors might work together. Obviously two being in the same place is comparitively unlikely, but it's feasable.
About the backstory in general. The inquisition doesn't generally have a strong local presence on planets, and it's more likely that a planet cut off for that long would have no inquisitorial presence (or maybe one 500 year old guy). If a world is hard to get to a problem may well be able to grow unnoticed - maybe they're just the first inquisitors to get to the planet for some time? Maybe they're lower rankers sent to assess the planet and are in over their heads. Plenty of imperial worlds are 'primitive' worlds with limited technological access. I've long been attracted to the idea of a campaign where the heroes are seperated from their favourite toys.
It's a good basic idea with no huge problems. Like all ideas it needs fleshing out, unless you happen to be good at winging it

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