If you have a frameset that is made up of left.htm top.htm and main.htm and you rename one of them it will throw everything sideways. names are critical in web design.
For example, index.htm is not the same as index.html
I imagine what has happened is that either you renamed the files which knocked things out of line or you haven't used the correct frameset instruction for your pages to display properly.
A normal hyperlink will not work for frames. You have to use a target="" tag to tell a page to load into the main content area of your site when you click a link. Failing to do this just makes your frame jump to a single html file instead of loading the page into your frameset.
This is just one of the delights of working with frames. You also have issues in getting a frame site indexed by search engines since your page is actually two, three or even more pages displayed as one - which one does the search engine pick ?
Then there's the problem that if someone links to your main content page, unless you embed a clever little script into it, it is quite possible to have it load on its own with no top or left panel in sight.
Don't you just love frames...
Using them means naming your main content frame area and pointing your hyperlinks to the page you want to load and naming the target to load the page in.
Without being able to see what it is that you've done it's impossible to say for certain what the remedy is, but I strongly suspect that your renaming of files and probably the lack of a target in the hyperlinks is at fault.