BREXIT has re-energised the campaign for independence but also “profoundly changed” what it must explain in any future referendum, according to a leading thinktank.

A report published today by UK in a Changing Europe says a Yes prospectus would need to confront “challenges” over the border with England, trade and the economy.

The authors, Professors Nicola McEwen and Katy Hayward, said there could be benefits from the SNP’s policy of an independent Scotland rejoining the EU, such as free movement for jobs.

However re-entry would also make Scotland’s border with England an external EU border which would need to be carefully controlled and managed.

Some cross-border arrangements envisaged at the time of the 2014 referendum would therefore “no longer be possible as a result of the UK’s departure from the EU”.

There would also be “behind the border” processes needed to regulate the flow of goods, services, people and money, requiring new technology, infrastructure and staff.

Nicola Sturgeon has said she wants to hold Indyref2 by the end of 2023, Covid permitting, but Boris Johnson has refused to grant Holyrood the power to hold it.

The First Minister has said she will legislate for a referendum regardless, but such a law would be challenged at the UK Supreme Court and probably struck down.

Ms Sturgeon has admitted there would be “practical difficulties” for trade over the border if an independent Scotland was in the EU, but insists talks with the UK could ensure business didn’t suffer.

She has suggested the protocol keeping Northern Ireland in the EU single market for goods could serve as a “template” for Scotland.

But today’s report makes clear the EU would be unlikely to allow such an arrangement, as the protocol was predicated on avoiding a return to violence in Northern Ireland.

“In the case of an independent Scotland, there should be no expectations of similar commitments to avoiding a hard Anglo-Scottish border,” it said.

“There is no history of recent political conflict centred upon the Anglo-Scottish border to focus minds on the desirability of avoiding a hard border.”

However it added the EU might allow Scotland a lengthy transition to set up border infrastructure before strictly enforcing its rules.

The report also said Scotland would have to apply to rejoin the EU and the “negotiations may be long and they would be difficult”.

However, on balance, the EU was likely to grant membership.

The authors said they had raised “critical issues” to ensure an informed debate on independence.

“It is vital that any detailed prospectus or white paper confronts the challenges that Brexit has presented, including the management of Scotland’s future borders,” they concluded.

Prof McEwen, of Edinburgh University, said: “Our purpose is to open up a conversation about the nature of borders, how and why they are managed, and the kinds of systems that we expect may be necessary under a scenario of independence in Europe.

“Rejoining the EU as an independent member state would open up Scotland’s borders to Europe, reviving opportunities for the free movement of goods, services, people and finance.

But at the same time, it would mean a new EU border between Scotland and the rest of the UK, requiring new processes, infrastructure and bureaucracy to oversee Scotland’s trading relationship with the rest of the UK.”

Prof Hayward, or Queen’s University Belfast, added: “The realities and complexities of titanic projects that change relationships between neighbouring countries can often become most evident at the borders between them.

Just as we have seen with post-Brexit Britain, an independent Scotland in the EU would change the ‘what, how and where’ of movement across its borders. This would have ramifications for Scotland’s neighbours as well as for itself.

“Such consequences are worth thinking through carefully, beginning with a purely academic exercise such as this, not least because the UK’s evolving post-Brexit relationship with the EU could conceivably mould its relationship with Scotland across the land border post-Independence.”