problems with templates
 

i have upgraded my vb from 3.6.8 gradually until 3.8.2, however the issue is some modifications i have done to templates such as navbar and footer makes the admin cp give me a message of templates needs updating. This update will cause all the changes i've done to dissappear. How can i update the templates to get rid of the message in the admin cp without removing the changes i have done to my vb.

P.S. I have 5 different vb styles so thats a lot of work to re do all the modifications again. Can any one help please?