I was just wondering if this will affect my database.
Yes.
Oh... you wanted details?
The biggie is ADO vs DAO (open up Ac2003 Help and search for those topics so you can find out what this does to you). Libraries will be different because, among other things, version differences crop up. I would advise that you use Access itself to help with the conversion, but with a specific strategy that will minimize problems later.
If you have a working Ac97 DB, open a BLANK Ac03 DB. Then try to import each object from Ac97 to Ac03. You can import objects (including relationships, I think) one at a time or all objects in a given category. Do tables first, then queries and references, forms, reports, macros, and modules.
DON'T try to actually convert the raw .MDB file. You invite about a bazillion "missing reference" problems. Doing an import rather than a conversion-in-place eliminates a (sadly small) percentage of these issues. Expect a few reference issues anyway.
Use the forum's Search facility to find articles on "upgrading" or "converting" databases. This topic has been addressed many times. You can also search for "missing references" because that is another condition that will jump up to haunt you.