Daniel,
there has been no bug introduced into the Get All Latest functionality as you are suggesting.
Indeed, the basic principle of the Get All Latest functionality - that it recursively calls Get Latest, for each version controlled package in the model - has not changed since its inception.
That's right, Get All Latest simply calls Get Latest for each package, one after the other.
Now, when EA imports a package from XMI, it must first delete the existing package and its content from the model, before it can re-import it from the XMI.
When the package and its contents are deleted, that can have an effect on other packages in the model.
All associations using elements that are deleted will also be deleted.
The elements that are deleted will also be removed from all diagrams on which they were previously shown.
EA simply cannot use elements that do not exist in the model.
When the elements are re-imported into the model, there are certain situations in which the previously existing associations can not be restored. Similarly there are some situations in which elements will not be replaced on the diagrams on which they previosuly appeared.
The order in which packages are re-imported into the model can have an effect on whether cross-package dependencies are correctly restored.
The Sparx Systems white paper on "Version Control Best Practices" details situations in which Cross Package Dependencies can be affected by XMI export/import, and gives some guidance on how to avoid and minimize the impact of these effects.
Daniel, you apparently have some understanding of the need to have all elements present in the model in order to resolve dependencies, but perhaps you didn't realise that forcing EA to re-import packages actually causes them to be deleted from the model before being re-imported.
Please DO NOT select the option to "force reload from XMI".
Those packages where new content has been committed to version control will be re-imported as necessary.
I believe this on its own will virtually eliminate the problems you are seeing.
We are currently working on some new functionality that will scan and reconcile XMI file content with the model DB, to "put-back" connectors and elements that are contained in the XMI, but might have been erroneously removed from the model, due to the order of re-importing packages.
Until then, please follow the guidelines in the Best Practices document.
I hope this helps,
Howard Britten.