How can I increase the 128 character limit of a menu path? I know there are patches to core, but they were never backported to Drupal 6 from what I can tell. 


Increasing path length to 255 chars
Menu path length is limited by the UI to 128 characters


How can this be overridden in a theme?
You should be able to fix this by using hook_form_alter() and override the default maxlength for the input field, and then change the field in the db to varchar(255) if it isn't already.

Another option would be to use a token value for the path and change the value on output using theme_menu_item().

Perhaps the best option after all would be the Custom Tokens module. I haven't tried it so I can't say if it works.

The downside with tokens is that you would have to make one token per URL, or possibly use a part of the URL if it's generally the same.