Why do some verbs combine the "y" and the "e" in the past tense, while others retain "ye"? For example, pay to paid, but flay to flayed?
Is there a rule for this change?
Any help would be appreciated. Thank you.
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While there is a rule, I'm afraid it's not a very useful one.
It originates in the history of English which once had several well-defined classes of verbs with different reasonably predictable changes for changes in tense, number and person.
The good news is that for the most part Modern English is much simpler, with the only productive form (that is, form used with new words) being the addition of -ed, perhaps after removing a final e.
The bad news is that the old ways left a mark on the English language both in terms of some words still having preterite and past participle forms that aren't just created from adding on -ed, and which have mutated in slightly different ways to each other, making these much less regular than the Old English equivalents.
And there are also some words that are more recent (pay came into Middle English from Old French, not Old English), that have forms modelled on one of these forms (pay/paid matches say/said).
Sometimes verbs moved from one form to the other as described here.
So, the "why" is in that history, but alas the "rule" became deeply inconsistent over the course of that history, so now they just have to be learnt as irregularities. The one good thing here is that it tends only to happen to the more common verbs (a word that wasn't well-known would end up mutating to -ed through people not knowing the "correct" way), so while it's a bit of learning up front, eventually you can be fairly confident that more advanced vocabulary will almost all be of the -ed form.