aakk9999 - 9:41 am on Jul 26, 2013 (gmt 0)
A robots.txt file entry will not stop Google from indexing urls, it will only stop Google from crawling the pages.
Whilst this statement as above is true, the robots.txt block may stop Google discovering other URLs that are generated from the blocked page. It often happens that from one leaked URL Google discovers hundreds/thousands other URLs.
A good example of this would be a page where a visitor is offered an URL with a date as a parameter. If you stop Google visiting the initial page by robots.txt then Google may not "discover" multiple URLs for the same content where only the date is different - and where a link to another page will change daily with only date parameter being different.
Back to OP question - it is entirely likely that a technical error in Joomla upgrade has resulted in ranking drop.
- have your URLs remained the same after the Joomla upgrade?
- is your site structure (navigation, and navigation type) remained the same or has it changed?
- I presume that these additional URLs indexed point to existing pages, but URL has some extra parameters (or changed parameter order)?
As JS_Harris said above, it would be better if these pages serve 404, or even better, 410 Gone (Google will drop these pages faster). Hence, is it possible that you change your .htaccess to serve 410 based on some unique string in URL for these pages? Of course, you would then need to remove robots.txt block in order for Google to request these URLs and sees 410 Gone.
With regards on how long it will take Google to sort out your site - it depends. In general, I have noticed that whilst the drop is usually "off the cliff" chart type, the climb back is "mild upward slope" type of chart. As these "new URLs" that Google has discovered are "low value", Google will not crawl them that often, hence it will take some time to re-process these URLs. And further, this also depends on your crawl budget, i.e. how often Google crawls your site and what is the average number of URLs that Google usually requests.