If I play Accompanying Flute and find only one Basic Pokemon, do I have to put it onto their bench?
No, since Accompanying Flute says "you may choose any number", you don't have to choose any Basic Pokemon if you don't want to.
Source: Twilight Masquerade FAQ; TPCi Rules Team (2024-05-23)

Relevant cards

Note: All applicable cards may not be listed below.
SV6_142
SV6_142