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This doesn't sound like a bug to me.
Best practices when working with an external drive are to make sure that everything using that drive is closed before removing it. In fact, you shouldn't have been able to eject the drive at all with something still open, which tells me you simply unplugged it - also a very bad practice.
If you remove a drive that has things open, you are risking losing data. That is just the way it is. It has nothing to do with any software, it is just common sense.
I would try doing a Save As, and save it to the local drive.
I would also highly recommend putting a second drive in the computer to store important client projects on, and only using an external device for backup and moving files to a different computer.
Regardless, don't just unplug external devices. Use the Windows utility to Eject them properly (it appears as a little green arrow in the icons next to the clock whenever an external device is plugged in). If the utility says it cannot eject right then, look to see if there are any files open, and then close them and try to eject again.
Yes, that's true, it is bad practice, I agree. But it's not that I always disconnect the drive on purpose. Sometimes it happens by accident. And it's just Flash that will DELETE that file on the next attempt to save and then won't let you anymore. That, on the other hand is Flashe's bad practice. I think it has also to do with why you shouldn't use flash in networks. The also may disconnect when the server shuts down and you don't expect it.
I can't put a second drive in my computer, because it's a laptop. I'd really like to do this also for a lot of other reasons, but there's not enough space.
Maybe I'll think about copying whole directory structures over there and back but that'll add a huge overhead to my working schedule.
It's just this destructiveness that really makes me go "wow." It would be still desastrous just not to be able to save the file, but deleting it before is quite cruel. And even if you manage to save it, a lot of library items get destroyed. I just can't see why all this damage has to happen. Well I'm still happy it doesn't format your hard disk for "punishment"
Once I just moved the laptop from the living room to the kitchen (I HAD to, don't ask why) and this got the USB drive to be disconnected for just one second maybe, NOT on purpose, the plug got loose a little bit. And poof, all the banners I was working on all got corrupted.
I mean, where does flash keep its data? In memory. or not?! Why should all elements get scrambled up in memory just because of a USB disconnect?! I am also a programmer and dealt with C++ and all that stuff, and most other programs at least don't mess up your whole work because of that.
I also think that people who work in big agencies with networks would really appreciate to be able to actually work directly on files in that network.
If that is the case with your working conditions/habits, then I recommend saving incrementally. That is, each time you save, save as, and name it with a new Rev. That way, if the external drive (or network drive in many users cases) gets disconnected you don't have to worry about losing a ton of data. This is also a best practice that many should be doing when working without versioning software, but few do.
And the whole delete thing seems strange to me, though I am not sure how that is working in the backend (no C++ on my resume, unfortunately). If there is something programmatically strange happening there, Adobe has a bug report page: https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform
Regardless, in the meantime all you can do is ramp up versioning to avoid the loss of data, and work to avoid accidental disconnects.
For instance, if you know you will be moving from the office to the kitchen with the laptop. Save everything, close Flash, and then move. This will add a couple minutes to the transfer, but saves your important data in the case of an accident.
I might consider some network attached storage as a secondary platform to work off of as well. Accidental network disconnects are typically less frequent than accidental cable disconnects, especially when you control the network.
Also, the internal drive of your laptop is a much more secure location to save files when working on them. Hard drive crashes are much much less frequent than accidental disconnects. If you are backing up your data regularly to an external hard drive, then the drive crash won't even make that big of a difference for the important data.