This is closely related to the question at https://answers.atlassian.com/questions/37057184, so I would link this to my answer there.
Regarding groups, the basic principle is the same: if import of groups is not disabled, new groups that did not exist in the target will be created and existing groups may be modified, if the configuration that comes from the source instance is different. No group will be deleted.
Attributes of groups that may be modified are the sets of users and groups that are direct members of the affected group. So, for example, suppose group "G1" is exported from the source instance and it has as direct members users "A" and "B". Suppose that a group with name "G1" also exists in the target and has as direct members users "A", "C" and "D". Then, the import of groups would detach users "C" and "D" from group "G1" and add user "B" to the its members. All these changes would take place in the target instance. The end result is that after the import, group "G1" in the target would be exactly the same as it was in the source instance.
There is an exception with groups "jira-users" and "jira-administrators": member users and groups will be added but never removed from these groups.
Anyway, feel free to add any comment or question if you still have any doubt.
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