I got new firmware updates 39.39 should i update

Best is to ask the support.

I downloaded a FLAC file yesterday.

I play it with the VLC.
But my old ears cant hear any difference to the mp3.

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But before starting discussions.
First take a look what your audio-card (device) maximum output is.
If the device is NOT able to transmit high resolutions its void.
May be the player can, but the sound card can not.

I use a Soundcore 3. I always update my firmware whenever it gets a new update. Is it bad for the speaker?

If the speaker works properly after the update it was a success, otherwise not. :rofl:

Updating is not bad for a speaker, and is more of a process question. Every firmware update contains some chance the update fails, or make something worse. So I would normally only update if you have known issues and the update fixes those issues. A.k.a “ain’t broke don’t fix”.