Transpose but not the sheet music

See this bit of the handbook. https://musescore.org/en/handbook/4/transposition#transposing-instrumen…

To ensure that I have understood what you are hoping for - I assume that you have a Musescore score that is written for a flute in C. You want Musescore to play the notes that are written in that part as if they were played on your high pitch flute. Therefore, you want the sound to played a major third higher than written.

Referring to the handbook section in the link above, you will need to specify the transposition as a Major third up. Musescore will retain the same played pitches and therefore the notes in the score will be transposed down a major third to compensate. If you are viewing your score with concert pitch not selected you will see that the key signature has been transposed as well - don't worry about that yet. You then need to re-pitch the notes back up a major third so that they look the same as you started with but will be played back according to the transposition you have set. To do that select everything on the stave use Tools>Transpose>By interval and select up a Major third. Make sure that transpose key signature is checked.

It is a much easier process if you start with the correct instrument and transposition. Then you can enter the notes at sounding pitch or at written pitch depending on whether you are viewing the score at concert pitch (in the first case) or not (in the second case).