If a plugin utility drops this extra data, it is gone from the plugin. Opening the plugin in the Creation Kit will not necessarily restore this information. Also, if the compression flag is set, then the data must be compressed. Having the compression flag set but providing uncompressed data will cause issues, likely crashing the game or the Creation Kit. We will not be flipping this flag in TESVGecko. If the flag is set, then the data will be recompressed when the plugin is saved.
That's the general overview.
UPDATE: The issues we found earlier were due to using the SharpZipLib port of zLib. This port does not include all of the zLib library. You must use zLib v. 1.2.3 to decompress/compress Elder Scrolls plugin data properly. This applies to all versions of Elder Scrolls and Fallout games up to and including Skyrim.
UPDATE 2: Sharlikran has picked up the development of TESVSnip. He and his team will be changing it so that it uses the proper compression library. You can follow their progress on the Bethesda forums.
Edited by AndalayBay, 01 December 2012 - 11:01 PM.