When Metaprofiles was originally configured with syncing a lots of data, then reconfigured, Metaprofiles GBL and GBP files will not reduce their size.
Behavior is by design
ER 226015 has been created to modify Metaprofiles behavior from 'merge' to 'recreate' the archive
Metaprofile files are actually a ZIP archives. The 'merge data' atcion is taken by default because same file may accomodate user data for when user connects to different machines. For example, use may get one set of Metaprofiles data when connecting to TS 2003 and another set when user connects to VDI Win7. User's MP files will accomodate both sets.