When I edit the 3D settings in the Nvidia Control Panel settings to improve the graphics of Minecraft bedrock edition, it also changes the same settings for Minecraft Java but that messes up the graphics in the Java version. There is no way to change the settings for one version without the other version's settings also being changed.
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I should add: The fact that the Nvidia control panel affects both Java and Bedrock is obviously not Minecraft's fault, but rather caused by the fact that Nvidia control panel works that way. If you want to configure the graphics card for both versions separately in the panel, that would need to be implemented by Nvidia, not by Minecraft.
Does MC-1794 describe your issue?