LG phones store their phonebook data in a way that makes it easy to synchronise and in particular tell if an entry is new or just changed. It does this by attaching a unique serial number to an entry. If you edit the entry, this number remains the same. If you create a new entry then it assigns a new number.
For example if you change an entry name from "Lauren Smith" to "Lauren Jones" and a work phone number (such as if they got married and a new job) then sync software can tell it is the same person and not a new entry. Sync software can also tell when entries have been removed. This also helps distinguish people. For example you may know two people named Tom Jones and sync software can the difference between there being two people or one person whose details get changed.
The numbers are allocated by the phone, starting from one. Erasing all your entries does not reset it back to one.
There is some sync software (notably that used in Verizon stores) that does not talk to the phone correctly. It transfers entries to the phone, but doesn't do so correctly and leaves the phone with entries with a higher serial number than the next one the phone will hand out to software that does synchronize properly.
Later on, as other software such as BitPim does correctly sync with the phone, the phone allocates new serial numbers that overlap those of entries already on the phone. You then end up with multiple entries with the same serial number.
When reading from the phone, BitPim will detect when entries have the same serial number, list which ones they are and refuse to read the phonebook into BitPim since the data on your phone is corrupt.
In order to recover you must erase the phonebook on the phone using the phone menus to do so. You can do this by doing Settings & Tools, System, Security, (your lock code is the last 4 digits of your phone number by default), Erase Contacts.
You will want to make sure you have written down or have all your contacts information in BitPim or some other program. You can also get some data from your phone. When BitPim lists entries with duplicate serial numbers, delete all but one of the entries. Repeat this until the phoneback can be successfully read and then reenter the entries you erased into BitPim. Erase the phonebook on the phone and then sync from BitPim.
Why not make BitPim fix the corrupted data?
You are welcome to contribute code that does so. It was other programs that corrupted the data in the first place so they really should be the ones fixing this.
I can see various files on my phone and can hack things that way
That is exactly likely what the programs that corrupted things did in the first place. This is why BitPim always tries to use the correct protocol as intended by the handset manufacturer since that will do all the necessary updates and tracking of relevant files and information for that phone. We only directly manipulate the phone internals when there is no other way provided by the manufacturer, and are very careful when we do so. The integrity of the data on the phone is more important to us than only getting a tickbox for a particular model in order to sell the program.
BitPim Online Help built 17 January 2010