If you're running into that problem, it implies that you haven't split
your application into a front-end (containing of the queries, forms,
reports, macros and modules), linked to a back-end (containing the tables
and relationships). Only the back-end should be on the server: each user
should have his/her own copy of the front-end, preferably on his/her hard
drive.
When you do that, then you can make changes to your heart's content
without any problems. Once you're happy that the changes are correct, give
each user a new copy of the front-end. (Tony Toews has a free Auto FE
Updater available at
http://www.granite.ab.ca/access/autofe.htm to help in
this regard)