In my experience with converting, there are no problems using the Tools ... etc. conversion method. Access 2003 makes a backup copy of your file first, and reports any conversion errors, so you can always get back to your original Access 2000 format file if necessary.
However, you need to remember:
-- In a multi-user situation, you can't convert unless all users have Access 2003 available;
-- It's a good idea to 'housekeep' your database, removing redundant reports, queries etc first;
-- Go to the Visual Basic Editor window, and choose the Debug ... Compile menu option. If any compile errors are reported, then your database will not convert correctly.
I hope that these notes are useful.
Bob Stubbs