It's not supposed to go into the 2 smallest cogs on the back when in the little ring (the system stops you because those gears are so inefficient)
If you're not getting the big ring I'd suspect you pushed the button on the junction box in a way that changed the shifting mode, so you've gone out of synchro
Best place to look for Di2 advice is here https://bettershifting.com/...hronized-shift-mode/

It sounds like it is in safety manual mode from fiddling around with the button on the junction box. From memory you need to double tap or triple tap the button on the junction box to go back to syncro mode there are 3 modes syncro non syncro safety or some other idiotic thing.

The number of times I have swore at di2 in the last month in lahti and nice when I suffered various black box type problems similar to you damaged cable etc hahahaha. When it works fantastic when it doesn't disaster

I never bothered with micro adjust much on the trainer just use 1 gear and erg.

Here's the mode info
You can change between the shift modes by double-pressing the button on your junction box. When you do this the bike cycles through three modes:

Manual mode - Indicated by solid red/green LEDs. This is traditional, full-manual shifting.
Shift mode 1 (S1) - Indicated by both red and green LEDs flashing twice. The default S1 mode is semi-synchro: automatically shifts the rear derailleur when you shift the front derailleur.
Shift mode 2 (S2) - Red and green LEDs flash three times. By default this is full-synchro and this automatically shifts the front derailleur as you shift the rear derailleur.

So turns out I'm even more of a newb than I thought... it needed charging!! I guess during this whole process the batteries ran low enough to stop the front derailleur.

Sigh.

But a good lesson for me and maybe this will help somebody else out one day :)

Damaged cable? There's the problem...if Shitmano got on their progress and kicked out a TRUE fully wireless system, no cables would be crimped. I've had 0 mis-shifts with my SRAM "wired" 10-speed (except when my R2C shifter's internal pawls stripped out). But yeah, no reason for wires in this day & age...c'mon Shimano, get it together...too slow for innovation...and yes, I'm going to upgrade & get rid of the cables this coming year!

Agree. Sram wireless makes much more sense the fragility of those di2 wires running through the cockpit down to the battery etc... Jeez what a pain

Depending on your chainrings, of course. If you are using 53-39 rings - or tell E-Tube that you are - you can uncheck the 'gear control' option and get access to the smallest two cassette cogs when in the small chainring.