Funny question. Make changes but be aware of update conflicts.
My first tipp is not to use automatic updates which can have fatal consequences (like the now 1.7.8.0).
My second tipp is to manually edit the header.tpl and footer.tpl in the httpdocs/pdf directory and use static data. If you want still automatic updates there is the possibility to remove write on these files and they can not be overwritten.
It is possible to upload a different logo for invoices in Prestashop -> Design but think it will help only for the logo. Mainly it is used to have a logo in another size/resolution but can be totally different as well. Other data like address and bank data and so on need to be static in the file if it is different from the shop data.
There is a system with override directories existing as well but not sure. Not trustable for me as my custom.css has been replaced with an empty custom.css by the first and last automatic update. So I don't set a penny on override directories.