Im pretty sure if you just copy all the contents of the stick it should be fine. If you are paranoid.. chose the option to"unhide" all files ( in Windows explorer tools) to ensure your PC copy is the same as the memory stick one
AFAIK, once you have copied your m2ts files ( at the appropriate size) that is it
The JVC Everios with thier MOD files also had an unusual no of files on HDD ( some backups , thumbnail files which were very small compared to the real *.MOD files) making it hard to know what to delete and what to keep but simple "mirrow ing your memory stick for reassurance should be all you need