The search files will not change. So for example, if you add the word "zebra" to the topic and only copy the topic to the server, searching for "zebra" in WebHelp Version 1 will not return the topic.
Similarly if you add index entries, those won't be available in the index.
A bunch of other behind-the-scenes files are also updated, but I can't say for sure what would be affected.
If you want to minimise the number of files copied to the server, use the Publish function and make sure the "Republish All" checkbox is NOT selected. That way, apage2.htm and apage3.htm are not copied, but all updated supporting files such as search and index are. (You continue to generate to the desktop, but the publish action copies files from the desktop to your server location.)