Here's my command line:
-8 -V --delete-input-file -w - -o %d
Does it matter what order it's in?
Using foobar2000 1.3.16 and flac 1.3.2.
You don't have any input file. You are encoding from a pipe. If you really want to delete input files and use flac.exe in combination with foobar2000, you need to use foo_run.