We recommend that you deactivate a user rather than deleting them, in case some applications contain historical data, e.g. documents that the user has created.
For example, a user may be a participant in a JIRA issue. If you remove the user from the directory managed by Crowd, JIRA will not be able to find the user details when referencing the issue. If you do need to remove the user from Crowd, you must first remove the user's involvement in any JIRA issues, as described in the JIRA documentation.
Read more about deleting or deactivating users in Crowd.