Letter writers outside the specific area of interest

[epicfail1]

Hello everyone,

Last year I applied and got placed in a mid-to-low-range PhD program, but eventually turned it down because I thought I could place higher. Professor A had unofficially supervised the project I used as a sample, but I had not asked them for a letter because they told me that they thought the three senior-level professors I asked for letters would write good ones. This year, I asked Prof A for a letter; they first agreed, and a month later, they informed me that they would not write me a "strong enough" letter, although they said it would still be a "good" one. Their reasons included 1) my turning down the mid-to-low range program without consulting them (they are a fan of that program) and 2) submitting a revised and resubmitted draft of the project I used as a sample (to a journal that asked for a revised draft based on the first submission) without having them read the final revised version first. My reasons for submitting the R&R without having them read it first were that they always give hugely inconsistent feedback and that I had to meet the deadline and could not make it on time for them to read it first. Therefore, I cannot ask Prof A to write a letter. 

The three senior-level professors have agreed to update their letters. They all encouraged me to apply again and agreed to incorporate whatever I felt needed mentioning to make the application stronger. But none of the areas of interest of these three professors directly parallel my proposed first two areas of research. For instance, I will say that I am interested in 1) metaphysics, 2) epistemology, and 3) social and political philosophy. My writing sample, which will be a shorter version of the article that is currently being reviewed by the referees for a second time, is at the intersections of metaphysics and epistemology. My letter writers mainly work in areas other than these two fields.

I was wondering if this would be problematic for my application. None of the letter writers can vouch for the skills I should have demonstrated while writing the paper under unofficial supervision. If I say that I am interested in metaphysics and epistemology, and if the letter writers can only merely mention the project on which my sample is based, and cannot talk about the project as a supervisor would talk about it, what does this show to the admissions committee? Would it raise red flags if none of the letter writers talked about the sample in detail?

Many thanks for the time you devoted to reading this. Cheers!