"Get All Latest" does not get all from latest packages

[ngong]

EA-SCC(-PTC) version control link:
Built an .eap file with the master package.
Issued "Get All Latest" - for 44 sub-packages, nesting depth is 3: master - view - package
Ran a query to find "External References", that is, missing links between elements in those packages: found more than 50.

Because I know, all the links shall be there I ran "Get Latest" on views: EA tells me that they are "up to date", but I checked "Force reload from XMI".
Forcing reload of one view solved 4 links, forcing reload of the other view solved the rest.

But not all missing cross references are related to connections: on some component diagrams components are missing. Force reloading of the containing package solved this. But how to find all diagrams missing elements, supposed to be there?

[ngong]

more details to the problem:

I lost several weeks of work and - that's worse - reputation in modeling by rolling back to older versions and manually had to re-enter change requests.
On check-in I used to use the window "Missing Cross References" too optimistically. It changed my model silently.
Currently I hope to survive and keep my model consistent in the following way - which is far not acceptable in the long run:

• When I check out a package, immediately I try to check it back-in again. I cancel that check-in anyway.
• If I get the window "Missing Cross-References" I also undo the check-out
• I have to analyse the situation prior to try to check-out the package for change again

and ...

• "Get Latest" on contributing packages. I can find the contributing packages by double clicking the count of missing cross references. A list of xmi:id appears.
  The xmi:id point to elements owned by contributing packages. How to identify the elements from their xmi:id is another story.
• But: Now I never click "ok" in "Missing Cross-References" unless I exactly know what they are about.
• Deleting the links by unchecking, or leaving them in - either may violate my model.