Yes, Candito, perhaps you can see that I and others above also have this problem of the intermittant appearance/disappearance of the Delete After Import option. Above you can see that Apple rep acknowledged my report with an unhelpful and mildly-annoyed-but-polite message. Too darn polite, those Apple support reps are.
I detect that Apple knows about the problem but doesn't know the solution.
The longstanding clumsy process of moving valued photos to your Mac needs streamlining. My wife has no patience for it, which means the burden of manager her monty gigabyte photo/video import falls on me. Given that this is 2016 and we Mac users pay a huge device purchase premium to support Apple's generally outstanding software and services, Apple ought to streamline it. The process of (a) open Photos and import-to-Photos, with most of us electing to also delete those photos from Camera Roll, then (b) open iTunes and Sync (copy) the same stuff back onto the iPhone, requiring human attention throughout the lengthy procedure, needs to be simpler. Perhaps Apple is busy working on a grand solution. That reason for fix delay we would all applaud.
Meanwhile, use Preview> File> Import (from device) to manually delete your photos from your iPhone Camera Roll. After Select All, use the obscure "delete" icon in bottom-left of the Preview window's info bar. Note, this procedure has potential for irreversible cockpit error, please first manually double-check that all of your Camera Roll already imported to Photos.