It’s not clear to me what you mean by
javascript defined in the header of the parent page no longer works.
The page was created on the server. Usually it contains javascript file urls
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
In this case, the "update" of javascript files can occur only in the client.
Check the html pages on the client. Are tags expected? Are there tags for all expected javascript files?
Using browser tools (such as Google Chrom developer tools) make sure all script files are uploaded.
If this does not help, it may be that the order of the script tags has changed between the first and second load. This may result in other javascript behavior being executed in the browser.
EDIT:
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