Change plist and make it stick

I don’t really know the right answer, but I have a guess.

You mention that you use safari on Windows, but you don’t mention the window’s version. In any case, the extreme load your computer had (in terms of RAM/HDD) might have caused a corruption in the Safari’s config and/or cache. Your computer, in an effort (desperate!) to save its information and write to the page file, might have had problems saving all the info before the shutdown actually occurred.

When you returned after the reboot, safari’s settings may have been corrupted preventing the TopSites button to appear.

I don’t know much about Safari’s architecture under Windows, but on OS X if the preferences are corrupted, we simply remove them and the program regenerates them upon first start.

This is just a guess of course.

But remember that your computer was struggling to save its state when you shut it down. You had no RAM and your pagefile was enormous.

I've carried my bookmarks with me after the first import ever since Safari 1.0 by just dragging/dropping the file into the Safari folder in ~/Library. Why did you go through the hassle of conversion?

Just backup the plist and drop it in place of the old or newly made plist whenever required.