No there will be no problem with that. This is what Crowd is designed for. Please make sure both jira instances have same directories mapped to them in order to ensure that Crowd sso works correctly.
Here you can find documentation about connecting jira to crowd https://confluence.atlassian.com/crowd/integrating-crowd-with-atlassian-jira-192625.html just add another jira. Depending on your use case you may map same directories to both jira applications in crowd (to ensure sso capabilities ) or map different dirs if you like. Here's a crowd webinar that describes more crowd capabilities https://www.atlassian.com/webinars/software/centralize-identity-management-using-crowd-data-center
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