I'd simply respond back to her with the maths.
Let's assume for ease that the GF flat is 1000 pm and the FF, 500 pm. The GF is rented full time, but occupancy on the FF is 50%.
Maintenance for both is 50 pm.
As stands the total annual income is £15k (1k x 12 plus 500 x 6). Less maint of £600, so you share 14.4k
Both of you then receive £7.2k annually.
Under her arrangement your annual income would drop to £2.7k (500 x 6 minus 25 x 12).
Meaning you lose £4.5k annually - over 60% of your rental income to subsidise her new living arrangements.
If she wants to move into the flat, then she should do so at market rates with the income and maintenance continuing to be divided equally.
She would also have a tendency agreement - as even though she is a "partial" landlord any rental needs to be legal between you both. This would give her no more rights than the current tenant.
In your case I'd outline the above (with real figures) in an email and tell her that before any decision is made that the finances need to be resolved and that you need legal advice on her tenancy agreement.