HDConfig doesn't erasy any data on partition. It only removes the partition from the partition list. Let's assume you have the following layout:
Part1 | Part2 | Part3
and you want to extend Part2.
You need to first remove Part3 to make some space for extending Part2. First of course you need to backup all the data from Part3, because it will be overwritten (partially) by the extended Part2. Once done, just remove the Part3 in HDConfig and you will get the following layout:
Part1 | Part2 | Free space
Then you can change the size of the Part2 partition and extend it in HDConfig. It will warn you that this will cause the data to be erase, but this is a generic warning. You get the following layout:
Part1 | Part2 (extended by for example 2GB) | Free space
Then you should reboot and run the system from CD. Part2 partition is not visible to the system, because SFS detects that the size of the partition doesn't match the filesystem data. Now you can run SFSDoctor and fix Part2 partition and get access to it again.