It is unfortunate that you have to go through this situation over which you have no control. Scopus and other indexing services have certain eligibility criteria which are madatory for inclusion in the detabase. They conduct periodical checks of journals that are already included in the database and if for some reason, they no longer meet one or more of the inclusion criteria, they are removed from the database. This is done to ensure that journals maintain their quality standards.
If a university or college considers only articles published in indexed journals as a criteria for promotion, they will definitey want the journal to be indxed at the time when they are condcuting the promotion process. It is natural for them to reject papers that do not meet this criteria. Most universities will not consider the fact that it was indexed at the time of submission of the article. Unfortunately, that is how the system works.
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