Hello,
Sorry to hear about your trouble, caututilaje.
Looks like I had the same experience four days ago (post meta data wiped out completely):
http://wordpress.org/support/topic/180354
As mentioned in my post, I was using version 2.1.4 of this plugin without problems but an upgrade to version 2.2.0 basically killed my site (it relied heavily on custom fields in posts).
While I am not an expert, my guess is that activating the latest version of the plugin wipes out all post meta data (which includes, if I am not mistaken, custom fields, categories and tags).
Here is what did NOT WORK for me:
2) Checking tables and repairing tables in database through PHP MyAdmin.
The data was simply gone - there was nothing wrong with my database or any tables within. As far as I can see, it does not corrupt the tables, just deletes all the post meta data.
3) Posting in this forum.
My post went unanswered for four (4) days. Maybe the author is on vacation and very few people are using this plugin...?
Here is what DID WORK for me:
My hosting company has daily, weekly and monthly backups. I emailed them and asked them to roll back my server to a previous restore point.
That wiped out all of my changes to the site after that restore point. I had to input (and in some cases research) all of my custom field data again so it took me about eleven hours to bring my site back to it's original state.
If your site is new with very few posts and/or very little post meta data, you may just be better off reassigning categories and tags yourself.
Again, I am NOT an expert. What worked for me may not work for you and/or may not be the best way to reverse the damage.
I am sorry to hear about your loss and I hope you can get your site back online faster than I did.
Best Regards.