Hi @Gary Spencer,
There are couple of questions in need to ask before I can suggest a solution. Do you have the same set of users between Jira and Confluence? Do you have the same username scheme between applications? (for example both Jira and Confluence have users with names like 'jdoe' rather than Jira have 'jdoe' and Confluence 'john.doe')
Do you want all of the users to be now in Crowd or only some subset? Were those users created manually or users accounts were created by users themselves using public signup?
If both applications contain same set of users, you can try using import feature as described here https://confluence.atlassian.com/crowd/importing-users-from-atlassian-jira-30736459.html and import users from one of your applications. Then as user matching is based on username itself, once you switch to Crowd directory in Jira and Confluence your users should still have access to it and history should be maintained.
I suggest testing how it works for you on some staging environment before rolling this up to production.
Instead of removing internal directories in both applications I suggest disabling them. for now. In general it is better to administer users in one place and not duplicate them across applications. The only exception is to leave a unique sysadmin in internal directory in Jira and Confluence so you still can have access to those applications even if Crowd application cannot be reached.
Hope that helps,
Marcin Kempa
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