I've had this issue since I began using the SalesForce Connect module. I suspect other folks have not because they did not have an SME creating wacky file names that needed as much correction.
the TLDR version is: don't change file names for topics that are already exported to SFDC if you are ever going to republish in the future.
Symptom:
When publishing to SFDC after the initial publishing, the publish fails and returns the SFDC error message in your build log of "ENTITY_IS_DELETED"
Occurs when:
Delete Stale Files is enabled for the destination
Use Bulk Export is enabled for the destination
One or more topics has had its name changed in Flare/Windows between exports
Workaround
Delete all new duplicate articles. (hopefully these were only drafts)
Restore deleted SFDC articles from the SFDC recycle bin.
Create new drafts from the deleted articles in the Knowledge Archive (Article Management module)
Publish these new draft articles (This is the SFDC "publish" action, NOT the Flare "publish" action).
Rename all changed topic files in Flare back to their original names.
Do not, whatever you do, delete the first iteration of an article published to SFDC before it is published on SFDC (SalesForce publish action). This deletion will be permanent and there will be no chance to rescue the original article from the recycle bin. The flare destination will forever expect to see the original article and won't, causing the Entity is Deleted error.
You will be in the same boat for a previously published article if you clear the recycle bin before you can restore it. If either of these happens, you must delete all of the related articles and create an entirely new destination to recover by uploading totally new versions of all of those articles.