As I believe I stated in my first PP, I'm not a lawyer. I am retired now but have been a highly qualified member of the Society of Trust and Estate Practitioners (including being a Committee member) since it's formation and have had a long career culminating in top level management of a dedicated Trust company advising trusts and estates on a daily basis.
You do need to contact a lawyer, but yes you can do two Deeds of Variation providing they deal with different parts of the estate.
I agree it can be difficult to use a PoA to carry out IHT planning as it can only be used in your mother's best interests. This is problematic but there are cases that have succeeded including this one:
"Historically a key difficulty with such applications has been how to argue that a substantial gift, on behalf of a mentally incapacitated donor, can in any way be in their best interests if the primary motivation is to mitigate IHT on their death.
However, the recent Court of Protection case of In the matter of JMA ([2018] EWCOP 19) demonstrates that these types of applications can succeed. The application was for various gifts totalling £7m from an estate worth £18.6m – including one of £6m to himself! The reason given for bringing the case was to reduce the burden of IHT on her estate for the benefit of JMA’s heirs as a whole – of which the applicant was the main one."
As I am not lawyer and no longer practising, I am not in a position to advise you, but I suggest you explore your mother's position in more detail. Would anybody loose out if the DoV was completed? Would it have any impact on her benefits or contributions to her cost of care? If so, it could be challenged as you cannot use it to avoid paying for care or to allow her to claim more benefits. That would definitely not be in her best interests.
You would be varying your father's estate and in that, the compensation is free of IHT so you can legally declare within the DoV that this variation has no IHT implications. It shouldn't therefore be of any interest to HMRC. A DoV that is not being used to reduce your father's tax would not be registered anywhere and is merely an agreement between the beneficiaries of the Will.
However, if anyone believes the PoA is not acting in the best interests of the donor or is abusing their position they can report this to the Office of Public Guardian, which oversees these roles. The Office of Public Guardian can investigate the actions of a PoA and can direct an official to investigate. The Office of Public Guardian can then choose to remove the attorney from the PoA if they have sufficient evidence to do so. In some serious cases, the Court can cancel a PoA or take action against the attorney.
So, I believe a DoV is assumed to be valid unless it is disputed and challenged - you need to work out who could or would know about it and challenge it (if anyone) and then decide what the consequences would be. In my view, it may be worth exploring that risk but only you and your fellow beneficiaries can ultimately decide whether the amounts involved are worth it and on your willingness to take that risk after taking proper legal advice.
PS. Just be aware that most lawyers will err on the side of caution and not advise you to do this! I come from a different profession where taking calculated risks and legally avoiding capital taxes was my raison d'être!