Please tell me my data isn't gone... lie to me even
I'm not sure I understand your question, or even what you did, but let's walk this through.

If all you did was to issue a cp -R /var/lib/mysql /path/to/backup, then this does not harm your existing data. 

It is also an incorrect backup method. Your backup itself is probably useless (unless all tables are MyISAM and you issued a FLUSH TABLES WITH READ LOCK).

What's further unclear is your description of .opt and .frm files. Is that all you got? That's strange, because you should have also got some *.MYD files, and some *.ibd files or an ibdata1 file.

Which storage engines are you using for your tables? What is the output of 

mysql&gt; select @@datadir;
mysql&gt; show global variables like 'innodb_data_file_path' ;
mysql&gt; show global variables like 'innodb_data_home_dir' ;


?

Last, I don't understand from your question whether data has been deleted from your webserver (containing your MySQL data).