Re-read tags by command

I have a script that uses metaflac.exe to remove padding from FLAC files - is there any way to tell Mp3tag to re-read the tags of the tracks instead of having to do it manually every time?

What do you mean? Removing the padding leaves the tags alone, doesn't it?
F5 reads all the currently loaded files again.
Ctrl-T reads the tags again.

Yes, and I want to do it without having to press F5 or Ctrl-T :wink:

You could modify you tool so that it does not only call the external program but after that has finished calls MP3tag again. That will probably work only if you treat one folder at the time.

That's exactly my question how to do that.
(I only treat one folder at once with the metaflac.exe).

I don't know how you call metaflac - you would have to supply that information.
Then there is the help that shows you how to call MP3tag with command line parameters:
you would have to combine these in a suitable batch file which then would have to be called as a tool.
As I think that Ctrl-T or F5 is much easier, I will not invest any more effort in this topic.