I can tell you that whatever the problem was before it was not due to the restoration, assuming that what you say about running the restoration to completion is accurate.
The .htaccess file is part of the backup archive itself, unless you explicitly excluded it from the backup. Since you did not say anything like that, I assume you did not do that.
When extracting the backup archive, the backed up .htaccess file is extracted as htaccess.bak. When you complete the restoration and click on the Clean Up button, one of the actions performed is renamed htaccess.bak back to .htaccess.
It does not even matter if you are using Kickstart or the integrated restoration in Akeeba Backup's Manage Backups page. You are using Kickstart both times. The integrated restoration is a Joomla UI skin of Kickstart with a lot of the more advanced options hidden away.
What could have gone wrong? Plenty.
First of all, if there was another file named htaccess.bak then the .htaccess included in the backup archive maybe could not be extracted. This is not a fatal error, and the restoration will proceed. However, when renaming whatever random htaccess.bak file at the end of the restoration back to .htaccess you may be renaming a file which doesn't quite work.
Renaming the htaccess.bak to .htaccess may also have not worked, depending on the ownership / permissions. You get a warning about that, but it's easy to miss when you've restored sites thousands of times and stopped paying attention at the final displayed message.
It's also possible that you chose to remove the .htaccess during restoration, or replace it with the default Joomla! file. Since your host puts the code to activate a specific PHP version and will use the default (usually very old) PHP version if this code does not exist, you may have simply ran into the simple case of trying to access your site under a PHP version it's not compatible with.
When you get an access denied error, just delete the .htaccess file, go into your hosting control panel, choose the correct PHP version (if it's not already selected) and access the site's backend. If that works, you can regenerate the .htaccess with Admin Tools' .htaccess Maker since you're already using it. The reason I had you redo the restoration is that I had no idea what exactly you had tried so far and I wanted to remove all variables. I could not know if you had an extraction issue, or didn't run the restoration to completion, or had a permissions issue you didn't catch, or missed a message. Having you redo the restoration more carefully now that you were asking me for help would ensure that any such issues would be caught, reported back to me, and I could help you. Apparently your issue was far easier and I could have told you to just regenerate it, but as I said I wanted to remove all variables.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
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