Handling excess Roth contributions with a negative NIA

In 2022 I contributed $6000 to my Roth IRA. My MAGI was enough to place me into the Roth IRA phase out. I did not realize this until 2023. I overfunded the Roth IRA by $1000. 

 

I completed a removal of excess contribution form with my brokerage and the net increase attributable was -$100 because the Roth IRA decreased in value after the contribution was made so $900 was removed from the account. 

 

How do I handle this on my tax return? Do I change the contribution amount on the IRA contribution forms from $6000 to $5000? Do I need to complete a substitute 1099R form since the brokerage did not send me one? I would like to address this now so I don't have to worry about it next year. 

 

(Round numbers were used to make the math easier)