I've had this same issue enough times to be frustrated by it. I'm not sure what ".4 will make this optional" means since it sounds like editing the metadata will make it optional to destroy the TOC, which I don't think was what you meant. But I cannot understand why Sigil would erase an existing TOC with no warning, especially when the TOS is working according to what rules I've seen.
But I've also had some experience when I simply opened a file in Sigil to add an image, and then found that it had wiped the TOC. I didn't edit metadata, just inserted an image...ug..
Love Sigil, but I think an update or quick patch to stop this issue would be very helpful until .4 comes out.