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Thanks for your question - I am Sam and I am one of the Uk tax experts here on Just Answer.
I am afraid you cannot transfer at this late stage and expect HMRC to treat this as an allowable capital gain share. If you had done this in previous tax years then it would have been accepted (with also any share of rental income that might have arisen)
In so far as the loss on the ISA - I would need to know more about the losses - as the act of taking them from an ISA would lead to a tax charge - and then if its a trading account - and this is not her main source of income then possibly the losses would not be considered.