Go to a bike shop... In all seriousness I would google how to do a full reset on your system if you have been playing with not a lot of idea. Make sure both your derailleur end stops are set correctly and then trim gears if you have to.

Check your derailleur hanger alignment.

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Strava

this....

or maybe this is a used bike perhaps...??? worn cassette or chain

I'm in the camp of going to a bike shop and being there while they adjust the Di2 so you and we learn what caused this.

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Indoor Triathlete - I thought I was right, until I realized I was wrong.

Is the alignment fairly easy? I will research it in the mean time.....
The bike is brand new, only owner. Maybe 6 months I’ve been riding. I also thought my chain may have been a bit worn, I’ve put a lot of miles on it.
I definitely want to learn more about the DI2 adjusting........

I tend to avoid working on the bike. However, after looking at on line videos and with the confidence that I'm not going to break something that costs money, I've gotten to where I can manage my DI2 adjustments.

Little things can toss it off. Changing cassettes of different sizes (that's a mechanical B screw adjustment). Taking the rear wheel off and on frequently to put it in the trunk, etc.

Once I got over my concerns that it was too tricky to work with, I put it in adjustment mode on the bike rack and check it every two weeks when I lube the chain, even it doesn't seem to need adjusting.

The more experience and frequency that you give to adjusting/playing with your Di2 the easier it will get.

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Indoor Triathlete - I thought I was right, until I realized I was wrong.

shimano chain? it makes a difference.
is it on forward? the printed side faces out.

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Andy Tetmeyer (I work at HED)

When weird shifting issue occurs with RD, e.g. skipping on certain cogs but not others, 90% of the time is the derailleur hanger alignment problem. So before you go on any other Di2 fine adjustment expedition, make sure the hanger is not bent.

Ok.... I didn’t even think about the removal of the rear wheel throwing off adjustments? I do this often as I’m riding my Wahoo Kicker and road back and forth.

I appreciate all the feedback I’m getting, even if it doesn’t fix my issue I’m still learning. I’ll be double checking everything from my chain, hanger to removal of wheel etc.

Spoke to a freind last night with some knowledge on DI2, and to sum it up I’ll be going to the LBS to get a tune up and learn some more about my bike.

I have a race at the end of next month and need this machine running smoothly.

Thank you again everyone for commenting on my post. I’ll keep you updated as to what is found to be the culprit. Hopefully it will help someone out in the future.

Thx Dave