I have the 1877 book – Doyne C Bell's “Notices of the Historic Persons Buried in the Chapel of St Peter ad Vincula” – which is a record of the 1876 Victorian renovation of the chapel with full reports of the excavations, examinations of the skeletons etc. I am going to write an article on this but in the place where they expected to find Anne Boleyn (in the chancel, in front of the altar)) they found the bones of a female “not lying in the original order, but which had evidently for some reason or other been heaped together into a smaller space”. Bell goes on to say that Dr Mouat examined the bones and “pronounced them to be those of a female of between twenty-five and thirty years of age, of a delicate frame of body, and who had been of slender and perfect proportions…”. No other female remains were found on that spot.

From reading through the records of the exhumations, there is no record of any of the bodies from the 16th century being found in coffins and it was thought that some coffins were purposely broken up so that more bodies could be buried at the Chapel. I'm not an archaeologist, but I'm not sure that the elm chest would have survived that long anyway.

The remains of the people exhumed from the chancel in November 1876 – including Anne Boleyn, Jane Boleyn, Margaret Pole, the Duke of Northumberland (John Dudley) and the Duke of Monmouth were put into separate thick, leaden coffers engraved with their names, date of death and the year of re-interment (1877) and then “placed in the respective positions in the chancel in which the remains had been found”.

Hope that helps.