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I'm really sorry to hear about your mother's situation. She might be able to file for the injunction for protection against domestic violence from another state (although it depends on the county, because some clerks require that the petition be signed in their presence), but unfortunately she would have to appear in person for the hearing on the injunction. A judge can impose a temporary injunction without a hearing, but in order to get a permanent injunction, she would have to actually appear and testify in court (much like she may have to appear to testify in the criminal case).
I am directing you to use this site as a resource...it is really comprehensive and very helpful for women who have been victims of domestic violence. It explains the steps for obtaining a court order in depth:
The site also provides information for the Florida Domestic Violence Hotline, which can connect her with an advocate in her county in Florida that can provide support and assistance for her as well:
Again, I'm really sorry to hear about your mother's situation and I hope that she is safe and able to work something out.