It seems quite straightforward to me in that if the result of the Referendum is as the Leader of the SNP hopes (and Scotland secedes from the Union and becomes Independent) then all Scottish Regiments should cease to exist in the British Army. Personnel from those Units and all Scottish Personnel in the Royal Navy and the Royal Air Force should be offered the opportunity to transfer to fledgeling Scottish Units or discharge from the UK Forces.
The composition of the Armed Forces which the new Scottish Government will require are of course a matter that the new Scottish Government will have to address.