It says a diverging tax and regulatory systems will create complexity for all although it may mean better state pensions for Scots and there are some other potential investment and savings arbitrage opportunities in the longer term.
Following the publication of the Scottish Nationalist manifesto for separation between England and Scotland, HL has analysed the proposals from the point of view of UK financial services and UK investors.
It says that the duplicate institutions created along with duplicate financial systems will mean more complexity.
Tom McPhail, head of pensions research at HL, said: "As well as the obvious costs of all these duplicate institutions, there is the un-quantified and potentially far greater cost of having to do everything twice. "Every bank, insurance company, financial adviser and investment manager North and South of the border will have to invest huge sums of money in running duplicate systems and training their employees to deal with two different regimes.
"To take just one simple example, if a customer wants to know what rate of pension tax relief they are entitled to, the answer will depend on whether they live in Carlisle or up the road in Dumfries."
"This all has a cost to investors North and South of the border; in simple terms a Yes vote would mean poorer returns in the future on Isa and pensions due to higher administration costs."
An independent Scotland would look to create its own financial institutions, according to the proposals, which could replicate bodies south of the border such as the FCA and FSCS.
HL says the some of the duplicates the manifesto looks to create, together with the current cost of their UK versions include:
· Financial Conduct Authority £432 million
· Pensions Regulator £49 million
· NEST pension scheme £240 million
· Pension Protection Fund £35 million
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However, one positive aspect for Scots will be a promised a state pension £1.10 higher than the planned new single tier state pension from 2016. Based on current average pension benefits and costs, HL estimates this would cost an additional £52 million a year to deliver.
It is also being proposed that the planned increase to the state pension age to 67 could be delayed North of the border. Under UK legislation it is planned to increase from 66 to 67 between 2026 and 2028. Based on previous research from the NIESR and the PPI, HL estimates that this could cost the new Scottish government £1 billion.
There may also be potential investment and savings arbitrage opportunities in the longer term.
Danny Cox, head of Financial Planning at HL and a popular regular commentator on London's LBC talk radio station, said: "For now, investors should carry on making as much use of their tax exempt investment allowances as they can; it has been confirmed that existing arrangements would be honoured North of the border in the future.
"A change to tax rules in the future could open up the possibility for investors to capitalise on preferential investment terms in one jurisdiction compared to the other, or perhaps seeing people move to benefit from preferential inheritance tax rules."
A vote for separation might unsettle the markets but HL does not expect to see any significant volatility.
An independent Scottish government would have freedom to vary income, capital gains and corporation tax rates. In the longer term HL says companies could relocate North or South and people changing residence could take advantage of preferential personal taxation opportunities. Estate agents, tax advisers and lawyers could all prosper in this new regime, says HL.