If you enter/exit a Factorissimo Factory while Robots are trying to return to you, they'll freeze and be "dead"
You can't do anything to them except for shoot them out of the sky.

That's unusual. They should come back to you as soon as you enter, if you didn't take off your personal roboports in the meantime. Did this happen in a factory that contains another factory?

I hadn't taken off any roboports.
And can confirm this happens for top level factories, and sub level ones too.

My test.
1. Place Factory
2. Have Blueprint with a few items.
3. Place Blueprint inside Factory
4. Immediately walk out.
5. Walk back in, frozen bots and new bots will be deployed to complete the job.

Edit:
I was running 0.13.15 and just updated to 0.13.16 with the same issue.
Running from a Standalone (ZIP) x64 install on Windows 10.

Tested it, this only appears to happen when there is a factory building on the same surface as the blueprints. This seems like an issue caused by Factorio improperly handling really extreme robot behavior edge cases that never ever appeared in-game until I added some bad entities such as zero-inventory zero-recharge-slot roboports, aka factory buildings.

So how should we work around this? I had the issue where I had robots removing stuff outside, and I walked into a factory. When I came back out, they were all "dead".

A simple fix would be to place a roboport in logistics range of the factory.

the way I found to fix this is by editing the mod, and making it so that the factory has 1 "slot" to hold robots... I also edited the construction area and made it a 1x1 area... The reason is that sometimes there's an area picking up / reparing a factory due to the 0x0 construction area :D