Penn had already used his influence with the king in favour of John Locke. On his return from Holland, he obtained a pardon for "such exiled Presbyterians as were not guilty of treason." One of these was Sir Robert Stuart, of Coltness, who on returning home found his estates in the hands of James, Earl of Arran. The two friends met in London, and Penn congratulated the restored exile. "Ah! Mr. Penn, Arran has got my estate, and I fear my situation is about to be now worse than ever." "What dost thou say?" exclaimed Penn, "thou surprises and grievest me exceedingly. Come to my house to-morrow, and I will set matters right." Penn at once sought the Earl of Arran. "What is this, friend James, that I hear of thee? Thou hast taken possession of Coltness' estate. Thou knowest _that it is not thine_." The Earl replied, "That estate I paid a great price for. I received no other reward for my expensive and troublesome embassy to France except this estate, and I am certainly much out of pocket by the bargain." "All very well, friend James, but of this assure thyself, that if thou dost not give this moment an order on thy chamberlain for £100 to Coltness, to carry him down to his native country, and £100 to subsist on till matters are adjusted, I will make it as many thousands out of thy way with the king." The earl complied, and after the Revolution Coltness recovered his estate. The earl had to refund all the rents he had received, less by the £300 he had advanced. This may be justice, but it was carried out in rather high-handed fashion.
At the Yearly Meeting in May, 1687, the Quakers at Penn's instance expressed their gratitude to the king for the declaration of liberty of conscience for England which he had issued in the previous month. Mindful however of the strain of royal power by which the relief was obtained, they inserted in the address this significant clause:--"We hope the good effects thereof for the peace, trade, and prosperity of the Kingdom will produce _such a concurrence from the Parliament_ as may secure it to our posterity in after times." The King in his reply to the deputation who presented the address, said he hoped before he died to settle it so that after ages shall have no reason to alter it.