When you say your tickets are out of the workflow - do you mean they have no status associated with them or that the status they are associated with does not have (an allowed) transition?
If it is the latter then the resolution provided by @Vasiliy Zverev should help you. Otherwise you need to create a new workflow with an outgoing transition from the status to Closed and then apply this in a new workflow scheme to the project to enable you to transition.
This may also be the bug where a JIRA issue forgets which workflow it is part of. Try moving the issue to another project or issue type with a different workflow, then move it back. Atlassian Support know about this
Also, try the integrity checker and check the workflow integrity. Some workflow issues can be fixed by the integrity checker, especially if it was caused by third party code causing an out of sync workflow operation.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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