Locked files are that way for two reasons. (Note it is the phone that has locked them, not BitPim). One is because their presence is fundamental to the operation of the phone, and if they were deleted would cause the fail to be unable to boot or operate. That covers files containing the ESN and stuff like that.
The other reason seems to be that the file is in use by a program running on the phone. There are usually all sorts of programs running such as SMS listeners, schedulers, contacts etc.
I believe there is a filesystem command to unlock files, but I haven't had the time to look into it.
So consider the whole thing a warning from your phone that they don't want you to change those files by directly overwriting them.
Can't I just offline my phone?
Taking the phone offline just means no unexpected external events will happen. For example if the phone wasn't offline and a phone call came in, the phone would have to look in your contacts to display the caller. If BitPim were busy updating the contacts then the display code may look at incomplete information and worst case crash. So the phone manufacturer just solves that problem by requiring the phone to be offlined while changes are made, and usually require a reboot afterwards since they don't want to deal with the internal programs re-reading the updated data.
BitPim Online Help built 17 January 2010