I have attached a sample mod to make this happen. The save is from the original run, where I had a "foo" and a "bar" logistic chest. A ghost and real entity of each was created. I then upgraded the version to 0.2.0, migrated "foo" to "qux", which is a container. When this version of the mod is loaded, the foo ghost is not migrated.
From the output it looks almost like the ghost is migrated, but then removed for some reason.
![Image](https://forums.factorio.com/images/ext/0041191a2282d213f3effe620c109e2f.png)