We've not heard of anyone with corrupted databases, and it's certainly not something that should be happening from us. Generally, corrupted databases are caused from the following 2 cases:
1) Your site is low on memory. If a page starts to load and is interacting with the database, but PHP runs out of memory, part of a SQL transaction may occur, but may not close properly.
2) Your site is low on disk space. The database file needs to be able to grow. If it runs out of space, the last few transactions won't happen.
There are plenty of other reasons, but those are the most common causes.
As for the comments, yes, you can use the XID method on just a few pages and all 'new' pages can use the href parameter. Basically, depending on how you're inserting the comments, you'll need to make a few minor changes to how your inserting them, depending on whether you're using the {JFBCComments} tag, the JFBCComments module, or the JFBCContent plugin to automatically insert them. Can you let me know the following, and we'll give you pretty straightforward instructions on how to recover the comments:
* The full URLs of the 4 pages that you want to recover from
* How you were inserting the comments on those pages (tag, module, or content plugin)
It shouldn't be too bad with just 4 pages
Alex