Change table prefix in MU

I’m sure I looked at all options on wordpress.org and most plugins for cause problems with MU. I believe its because changing wp_ messes up all the sub sites prefix that are wp_# ( should have been wp_sub# or something like that). Anyway the my host says I’d have to do this manually via search and replace or individually but I see this in wp_config. /**

* WordPress Database Table prefix.

*

* You can have multiple installations in one database if you give each a unique

* prefix. Only numbers, letters, and underscores please!

*/

$table_prefix = ‘wp_’;

If I change it will it only affect sub sites so I can then easily change wp_ everywhere later ? What problems may changing tables on a long functioning heavily edited site cause?