Yes, for the most part.  When downloading updates you have the option to go in and preview and choose/lock every field that can be updated.  Note that copying and pasting from one profile to another does not lock that profile, so if you have fields you don't want to be overwritten make sure you lock those fields.

Quoting Lewis_Prothero:

Quote:
The "Automatically lock all changed items"- option is preserved and has to be manually unflagged once you don't want it anymore.

Flagging it may lead to unwanted results (e.g. a minor custom change in the cast list will prevent all future cast-updates from downloading).

But I'd say that is better to having your custom data overwritten and lost.  At least with it being locked you can update the information at a later date.

When I download updates I preview them all to make sure I only take over what I want.  But I have to do this every day or so it isn't overwhelming, if you put it off for weeks or months and have a large collection and can be daunting to go through them all.