In late 2016 I applied for a re-entry permit and moved out of the US. In 2017 and 2018 I worked abroad for a foreign company. As of 2019, I'm back and working in California.

California is the only US state I've worked in, the state I'm USCIS-registered in, the state that issued my DL, and everything else. I have never lived in any other state.

We all know that California is pretty aggressive when it comes to tax collection. This year, it appears I could file non-resident in CA (not federally; I've filed my 1040 already). I'm basing the CA possibility on their "safe habor" rules:

The safe harbor provides that an individual domiciled in California who is outside California under an employment-related contract for an uninterrupted period of at least 546 consecutive days will be considered a nonresident [...]

So okay, cool. I meet that.

My question then, is: with regards to a future naturalisation (and, possibly my current green card status in the eyes of USCIS), is it safe to file a 540NR?

Or, should I file 540 as normal, and take the hit on my international income?