Replace is only available if used in VB, not in SQL, and yes, as it is executed in Access, the function has to be there to be able to use it. Thus it is no TSQL anymore.
Since you have a very simple replacement here, you can use the mid function:
update document
set file_directory = '//server2/' + mid(file_directory, len('//server1/')+1, 255)
where file_directory like '//server1/*'
The length of 255 chars is arbitrary; if your paths exceed that length, increase it.