This still sadly occurs in 5.2, and it's one of the most frustrating things. Does anyone have any information on which version this is supposed to be fixed for?

This issue seems to be related to #652856 which is listed as resolved in a future version. Does anyone know what version this is resolved in and how?

if the functionality is as EXCLAMATIONMAREK describes then most serious package development will be halted. If you have binaries or anything else that needs to be edited externally for your plugin it will loose it's GUID and no longer properly update. My team has also run into SVN issued where the GUID is occasionally lost, making team development of a package unreliable.

If not the suggestion offered by EXCLAMATIONMAREK could we get some way of manually linking the old GUIDs to the new or some such so that we can continue developement?

Noticed the same thing, but this only happens when the GUID of the files are different. The .unitypackage will store GUIDs of objects, so if each version of the package is made sequentially and applied to the same project, you should be fine. But if at any point you loose your meta files, or import the contents of the package to your project *not* from the package they may get different GUID, and getting an updated package will create the issue you described.

With that said, if would be really nice if upon importing, there was an "Override GUID" option, which would overwrite the current files, and assign the same GUIDs to the ones in the package.