How does score submission and selection work?

Noob to etterna so I’m not sure I understand some things. I have previously set a score on the song and my rating is 23.96. I play that song in the future for fun and do worse than my previous score. My rating drops to 23.92 and online the score displayed for the song is my most recent score… In osu! It only takes the highest score so I am very confused.

This is likely a combination of how the system works and a bug in the calculator. When submitting scores, the highest rated score is always accepted even if the percent is lower. This causes/solves issues where you can get higher ratings for lower percents. That is a bug in the calculator. On top of this, it is possible that you really did get a higher rating on the file and the score is accepted, but the skillset that the higher score was set for is much different than it was before. The skillset ratings are calculated by skillsets, and the scaling for those each specifically has the same bug.
So for example it is possible to get a 94.5% worth 23 overall having a 22 stream and 23 jumpstream, but then get a 94.6% worth 23.2 overall having a 23.2 overall and 22 jumpstream. That sound illogical and it is indeed mostly due to the calculator bug.
The skillset rating calculation for a profile takes each personal best for every rate. So now the 94.5% is gone and it’s worth more stream than jumpstream. So the rating of the jumpstream skillset drops and the stream skillset goes up instead. This in combination with all of your other preexisting scores can cause your rating to drop when you get a better score.

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That makes a lot of sense actually, thanks a lot poco0317. Does this mean that misses in different spots mean different things? Say i miss in a stream one run and then miss jacks the next run, does this alter the specific ratings?

The output of the scaler is completely predetermined by the calculator and then based on the percentage you get on the file.

You give a percentage and it gives a number. No replay data involved.