"Automatic size conversion" with .sav files with M3 Sakura?

I'm trying to take a save file from one version of a game to another—while this works with Wood R4 perfectly, it doesn't with Sakura because this process ends up corrupting the save file.
Is there any way to disable this, or to get around this?

Convert it for Sakura?http://www.shunyweb.info/convert.php

Most of my M3 Sakura games use .sav as a file extension.
Converting to any of the formats on that site gives me the original problem.