Sorry to keep answering myself, but I found a solution via metaflac used in a batchfile, that seems to work.
@echo off
title Reduce padding in FLAC - all files in directory
for %%i in (*.flac) do (
echo Removing padding from "%%~ni.flac" ...
"\metaflac.exe" --remove --block-type=PADDING --dont-use-padding "%%~ni.flac"
if ERRORLEVEL 1 goto error
echo Adding 4096 bytes of padding ...
"\metaflac.exe" --add-padding=4096 "%%~ni.flac"
if ERRORLEVEL 1 goto error
echo -- Done
echo.
)
echo.
echo -- Padding reduced
goto end
:error
echo.
echo ---- ERROR REDUCING PADDING ---- batch process stopped
:end
echo.
pause
exit
Save this as f.i. "ReduceFLACPadding.bat" and place in the right-context-menu folder of explorer. This will reduce any oversized padding in all FLACs in the directory to a standard 4096 bytes, leaving the existing tags intact.