The verb treat in the sense of entering into a negotiation with someone toward a particular end was part of the Middle and Early Modern English lexicon:
…and therefore, I conseille, that ye sende youre messageres, swiche as ben discrete and wise, unto youre adversaries, telling hem on youre behalf, that if they wol trete of pees and of accord, that they shape hem, withouten delay or tarying, to come unto us. — Geoffrey Chaucer, “The Tale of Malibee,” The Canterbury Tales, 1387–1400.
Besides negotiating for peace, the online Middle English Dictionary shows other complements: one could “trete” between two people as a negotiator, negotiate a truce, a treaty, the provision of a ship, debt resolution, or a marriage. One could also “trete” oneself out of one’s rights. The verb was also used intransitively.
In Lydgate’s retelling of the story of Oedipus and Jocaste, a delegation goes to the queen to urge her to marry:
For which the lordës all br oñ assent
with-Inne the touñ / set a parlament,
Shortlye concludyng / if it myght beñ,
Prudently to trete with the quene [Jocaste]
To condescende / be way of Mariage,
She to be Ioynëd to this manly knyght [Oedipus] — John Lydgate, Siege of Thebes 763–769, 1420–22.
Given the difference in status, the delegation is entreating the queen to marry rather than negotiating with her.
Shakespeare uses the same treat of construction, but with a more general object in the modern sense of ‘to hold diplomatic talks’:
Faulconbridge: And once dispatch'd him in an embassy
To Germany, there with the emperor
To treat of high affairs touching that time. — History of King John, 1,1.
In current usage, treat in this sense has almost completely narrowed to a fixed collocation, though with a change of preposition: treat for peace. The frequency of the expression, however, began a steep decline in the first decades of the 20th century.
Soon after its departure the first mission reported back with news that the English king was advancing towards Scotland with his army, forcing William to issue a fresh military summons. With his kingdom made vulnerable by his indecisiveness, William had no real alternative but to treat for peace. — Richard Oram, Alexander II: King of Scots 1214-1249, 2012.
Treat as negotiate also remains a part of legal language in England and Wales. In a compulsory purchase — in the US, eminent domain — a Notice to Treat is issued to a property owner to negotiate compensation at fair market value. In contract law, an Invitation to Treat — US: invitation to bargain — means to enter into non-binding negotiations.
The en- prefix will have had little to do with the divergent histories of treat and entreat, since words borrowed from Latin, with or with a French intermediary, don’t often preserve the meaning of the prefixes, i.e., no one who enters into an agreement senses the verb and preposition together are a tautology. And it is a rare case where anyone can determine why meanings evolve over time. The narrowing of treat is likely because other uses such as treating someone to lunch, treating a topic, or treating an illness began to occupy so much lexical space that there wasn’t much room left for treat as negotiate, and it disappeared from common usage.