No, for actual kits that has been patched into the .img files, you would have to restart the Master League. PES saves the team's data as it was when you started the ML, and that is the way it's going to be throughout the whole career.
I don't know about KitServer patches, but I wouldn't hold too much hope for that either.
And editing kits/squad numbers during end of year negotiation periods only applies to older versions of PES, the newer ones such as PES 6 and 2008 allows you to edit whenever you feel the need to.
But even this is the case, you would have to start again due to the fact the new kits is linked to the image within cv_0.img through some Hex_Editing in cv_1.img and this data isn't stored within the ML save files.