That happened to me once with Thunderbird. Not gone exactly but I thought they were, I had to right click and Compact the Folder I think it was because when you delete emails apparently they are not completely gone taking up space so compacting removes they totally. (I think).
But in the 4 years I've used Thunderbird (inbox shows June 05) that only happened once and like I said the emails were never gone and are still there to this day.
So yes I use Thunderbird
