For those couple of pages that you updated, I actually would delete the index.html files from those page folders on the web hosting account. That way when you are testing everything, you can make sure there are no issues. Click around, make sure everything is working. If you have any links that are linking to those pages, make sure those links work as well.
If everything is working ok, then proceed to update some more pages, until you feel comfortable updating all.
If you encounter any troubles along the way let us know.
This is new in the first beta of 3.0 and is mentioned in the announcement of this version (13 July):
Components that require PHP will now prompt to switch page extensions
In the manual of the Gallery Pro component, under Requirements, it says now:
‘Hosting with PHP support; pages containing Gallery Pro are published as PHP.’
I believe before version 3 the manual stated that you had to change the page extension to ‘php’ manually. As far as I know, this component has always required ‘.php’ as the file extension. It is a pity, though, that this only became clearer from version 3 onwards and it was only then that the process was automated (but only for new pages).
Edit:
In the manual of the normal Gallery it is not as clear. The only thing about PHP is this:
