The fate of precious Tudor stained glass marking the union of Henry VIII and Anne Boleyn is in dispute after its last-minute withdrawal from a private auction, the Observer has learned.

Urgent intervention by conservationists prevented the sale of English glasswork “of exceptional importance”, including a window made in the 1530s as well as older ­medieval glass. The windows were hanging in a 16th-century Dorset manor and were destined for a private contents auction until spotted listed alongside vintage furniture and china.

The rare stained glass lots were pulled from the bidding after a visit from Historic England and on the advice of the local council’s conservation officers. The “roundels” of heraldic glass have remarkable historic and cultural significance, according to experts, but were to have been auctioned in a clearance ahead of the sale of the whole of Sandford Orcas, a Grade I-listed building and a popular candidate for the title of England’s “most haunted house”.

On a site visit Dorset Council officers “noticed historic stained-glass roundels and a coat of arms had been removed, despite both these items being considered part of the listing,” a spokesperson for the local ­authority said this weekend. Removal would require listed buildings consent.

One of the more important ­windows is thought to have come from Nonsuch Palace, Henry VIII’s lost royal hunting base in Surrey. Built for him in 1538, the palace fell into disuse and only foundations remain. Many of its spectacular fittings and decorations are now dotted around Britain, adorning stately homes.

Guy Schwinge of Duke’s, the auctioneers handling the sale, said the glass roundels were not “fittings” but were suspended from wires.

He said Historic England backed this view and he had “no idea why” Dorset council “chose to ignore the advice and requested the stained glass be withdrawn from the auction”. He emphasised that Duke’s “immediately complied” and had been in further consultation with arts and heritage bodies.

Sandford Orcas manor, in the village of the same name near Sherborne, is itself up for commercial sale for the first time since 1736. Set in 73 acres of gardens, woodland and pasture, it had a guide price of £6.5m when it went to market.

Only two families – the Catholic, royalist Knoyles and the Medlycotts – have occupied the manor since it was built in the early 1530s in what the writer Arthur Mee, editor of The King’s England, described in 1939 as “a green lap surrounded by hills and reached by a sunken lane”.

In March 1966, Country Life called it “one of the most charming manor houses in the West of England”, but according to the Haunted Britain and Ireland website, it is “an eerie-­looking building, the grey stone walls of which give the appearance of being every inch the haunted house of tradition”.

The crowded ghosts in residence reportedly include three ­mysterious ladies in red, white and black, along with a farmer in a white smock, a Georgian footman, a fox terrier and, perhaps most tellingly, a young man staring at a stained glass window, as listed in the book Paranormal Dorset.

The previous owner, the late 9th Baronet, Mervyn Medlycott, was a known sceptic when it came to the haunted status of his home, once suggesting it had been “a nice, cheap way” to draw visitors. The baronetcy became extinct with his death three years ago and the property passed on to his niece, Kim Oliver, and her husband, Gavin Beard, from Brighton.

Neither responded to the Observer’s requests for comment, although a representative described her “as a private person”. It is not clear if the glass will be returned to the manor, privately sold, or go to a museum.

Window fittings and panels are protected in a house with such strong heritage status, but the laws are ­different for decorative items, or “chattels”. Jasmine Allen, director of the national Stained Glass Museum at Ely, explained what can be at stake if rare items are removed from context, even if they are not original features.

“It is a criminal offence to undertake works without permission, but aside from that, with any portable glass that bears heraldry, there is also great historic value because of what it can tell us about patronage, allegiances, marriages and hierarchies.

“Moving items can prevent the understanding of the whole history of a place.”

The rest of the sale went ahead last week. Medieval glass roundels of the Virgin Mary and the head of a saint were sold for £6,000, more than eight times their upper estimate.