If you and your partner are both named on the Tenancy Agreement you have with the Council then you should not change the locks. If you do, you run the risk of your partner applying to the Court for an injunction against you. In effect you would then have to give your partner a set of the keys. This would merely result in the expense of changing the locks being lost. There is a possibility that your partner wouldn't apply for an injunction, but I would imagine when someone no longer has anywhere to live then they would investigate all avenues.
If you are the only named person on the Tenancy Agreement then you can change the locks and your partner will not able to obtain injunction as they do not have any interest in the property. If the tenancy agreement states that your partner is also to live at the property (even thought he is not named as a tenant) then the Council may seek to rehouse you if they were to find out that your partner has moved away from property.
If you are both on the Tenancy Agreement with the Council and you no longer wish to be housed with your partner then you could serve a Notice to Terminate tenancy to the Council (your tenancy agreement will state the notice you are required to give and you should make sure you comply with this). At the same time you could ask for a new tenancy on the property in your sole name. The danger is that the Council may reassess your housing needs based upon the fact that you are separated from your partner and seek to rehouse you in a smaller property.
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