Dunno who you are replying to.
Anyway, isn't the following what was intended?
PS C:\tmp\output-dir-test> dir
Directory: C:\tmp\output-dir-test
Mode LastWriteTime Length Name
---- ------------- ------ ----
-a---- 2023-12-20 09:18 13303886 wavefile1.wav
-a---- 2023-12-20 09:18 13303886 wavefile2.wav
-a---- 2023-12-20 09:18 13303886 wavefile3.wav
PS C:\tmp\output-dir-test> flac --output-prefix=".\prepre" .\wavef*.wav
flac 1.4.3
Copyright (C) 2000-2009 Josh Coalson, 2011-2023 Xiph.Org Foundation
flac comes with ABSOLUTELY NO WARRANTY. This is free software, and you are
welcome to redistribute it under certain conditions. Type `flac' for details.
wavefile1.wav: WARNING: skipping unknown chunk 'LIST' (use --keep-foreign-metadata to keep)
wavefile1.wav: wrote 6621322 bytes, ratio=0,498
wavefile2.wav: WARNING: skipping unknown chunk 'LIST' (use --keep-foreign-metadata to keep)
wavefile2.wav: wrote 6621322 bytes, ratio=0,498
wavefile3.wav: WARNING: skipping unknown chunk 'LIST' (use --keep-foreign-metadata to keep)
wavefile3.wav: wrote 6621322 bytes, ratio=0,498
PS C:\tmp\output-dir-test> dir
Directory: C:\tmp\output-dir-test
Mode LastWriteTime Length Name
---- ------------- ------ ----
-a---- 2023-12-20 09:18 6621322 preprewavefile1.flac
-a---- 2023-12-20 09:18 6621322 preprewavefile2.flac
-a---- 2023-12-20 09:18 6621322 preprewavefile3.flac
-a---- 2023-12-20 09:18 13303886 wavefile1.wav
-a---- 2023-12-20 09:18 13303886 wavefile2.wav
-a---- 2023-12-20 09:18 13303886 wavefile3.wav
PS C:\tmp\output-dir-test>