Musical notes may be used to conceal a secret message in a way other than by substituting musical notes for letters (as proposed by Thicknesse, for example). There is record of a sheet of music which, when folded in such a way that the bottom portion is laid over the middle to be contiguous with the top portion, reveals a message: "Conceal yourself; your foes look for you."
However, some sources say it was sent to Charles II after the Battle of Worcester (1651), while others say it was sent to Charles Edward (Jacobites' Charles III) after the Battle of Culloden (1745). Moreover, there are two different versions of hiding the message in musical notes.
A facsimile is catalogued in WorldCat and Google and is given a date 1830. But it does not identify the recipient.
tonybaloney presents a sheet of music said to have been sent to Charles II by a loyalist lady.
It is made to look like a song set to words of loyalty:
"Tho I scorn to fawn or flatter yet my heart is ever true all inconcious of the matter you reject a prize
your due take me try me when you will faithful you will find me still."
However, folding the sheet such that curls attached to the stem of the notes on the top staff meet those for the bottom staff reveals a warning message:
"Conceal yourself. Your foes look for you."
A short article "Secret Message Sent to a King" in Times Dispatch on 8 May 1904 reports what "is supposed to have been the original secret communication" sent to Charles II at Boscobel after the Battle of Worcester was put on auction but was withdrawn. During the English Civil War, Charles II met a disastrous defeat at the Battle of Worcester in September 1651 and the king stayed in Boscobel for some time before he eventually fled to France.
Proceedings of the Dorset Natural History and Antiquarian Field Club (1921) (Internet Archive), vol.XLI, p.xxxvi, has a report about the provenance of this musical cryptograph.
W. W. Rouse Ball, Mathematical Recreations and Essays (1892 1st ed.,1914 6th ed.) (Internet Archive, p.402) prints the following version and says it was sent to Charles Edward, the Jacobites' Charles III, after his defeat in the Battle of Culloden in 1745. Although the previous version is to be folded such that the second line of the lower staff is aligned with the fourth line of the upper staff, this version is to be folded such that the fourth line (labelled "C" below) of the lower staff is alinged with the fourth line (again labelled "C" below) of the upper staff.
This item appears to have had attention around 1890.
The Archivist (Google), vol.I, no.4 (1888) reports the Stuart Exhibition being then held in London. But the "two lines of music" (No.995) is said to have been sent to Prince Charles Edward and the item was lent by Col. Macpherson of Cluny. The catalogue of the Exhibition is found at Google.
The item lent by Macpherson is cataloged as No. 565 in the archaeological collection (Google, Google).
The Royalist (Google), vol.1 (April 1890-April 1891), p.139 also mentions the item in the context with Colonel Macpherson of Cluny and Culloden.