The easiest way to fix is to use Library Tools > Convert Format.
The Convert Format Action Windows will show up in the bottom left of the screen.
Choose FLAC Encoder
Click Options, check "Apply DSP," click DSP Settings, click Parametric Equalizer, Add Mix Channels and swap left and right.
You can save the converted file to the directory of your choice. It will make a new FLAC file. You can move it to the same folder as the original file. Delete the library entry of the original file and import the new file.
You can tag all the files you want switched, show them in a View, select them all, and then covert them all at once.
Personally, I would use an external tool to permanently modify the FLACs in question so that L and R are in their correct orders. FFMPeg can do it from a command line.
Takes just seconds to do in JRiver.
