Missing Specs Error - Details about Build and Deploy Process?

My enterprise countered a scenario where we would like to learn more low level detail about the build and deploy process. Here is the scenario we encountered:

Given the circumstances of our schedule, we performed a full package build on Wednesday. On Thursday we created, via the batch versions web application, a new version of a report. We could successfully submit the report on Thursday. On Friday, we deployed our full package (built Wednesday). On Saturday, when we tried to execute our newly created version of the report (created Thursday), we received an error stating that the specs could not be found.

This is why we want to know more about the build and deploy process. Did the deploy wipe out, or overwrite all the exiting specs? How are specs referenced or retrieved when attempting to run a batch version? What table is this information stored on?

The Oracle document:
Package Under The Covers - EnterpriseOne 8.12 Application Release Level Onwards [ID 652833.1]

When you created a new version using the web client, that version was not stored on the deployment server. When you deployed a full package, your web-created version was lost. You need to create, check-in, promote, and deploy the new version.

A lot of this depends on what version of E1 and the Tools Release you are running. When the web client was first introduced, there were "web-only" versions. Lately, this distinction has been removed, and now there are just versions as before, needing check-in and promotion.

So, what is your system information?