If $y^2-x^2\bigm|2^ky-1$ and $2^k-1\bigm|y-1$ then $y=2^k$ and $x=1$ Suppose that $k\geq2$ and $0<x<y$ and $y^2-x^2\bigm|2^ky-1$ and $2^k-1\bigm|y-1$. Is it necessarily the case that $x=1$ and $y=2^k$?
Equivalently (I prove equivalence at the end): Suppose that $k\geq2$ and $m\geq1$ and suppose that there are two positive divisors of $(2^k-1)(2^km+1)$ which average to $m(2^k-1)+1$. Is it necessarily the case that $m=1$ and that these  two divisors are $2^k-1$ and $2^k+1$?
I've tested this up to $y\leq10^{10}$ but I haven't been able to make much progress with standard number theoretic techniques.
If $k=1$ then there are infinitely many solutions of the form $x=y-1$.

Let $(1)$ be the initial version of the problem and let $(2)$ be the supposedly equivalent version of the problem.
$(2)\implies(1)$: Suppose that $k\geq2$ and $0<x<y$ and $y^2-x^2\bigm|2^ky-1$ and $2^k-1\bigm|y-1$. We can write $y=m(2^k-1)+1$ for some $m\geq1$. Then
$$2^ky-1=2^k(m(2^k-1)+1)-1=(2^k-1)(2^km+1)$$
so $y-x$ and $y+x$ are two positive divisors of $(2^k-1)(2^km+1)$ which average to $y=m(2^k-1)+1$. By $(2)$, $y-x=2^k-1$ and $y+x=2^k+1$. Then $x=1$ and $y=2^k$.
$(1)\implies(2)$: Suppose that $k\geq2$ and $m\geq1$ and suppose that there are two positive divisors of $(2^k-1)(2^km+1)$ which average to $m(2^k-1)+1$. Let $y=m(2^k-1)+1$. We can write the two divisors as $y-x$ and $y+x$ for some $0<x<y$. Thus,
\begin{align*}
y-x&\bigm|2^ky-1,\\
y+x&\bigm|2^ky-1,
\end{align*}
since $2^ky-1=(2^k-1)(2^km+1)$. Manipulating these divisibility relations shows that
\begin{align*}
y-x&\bigm|2^kx-1,\\
y+x&\bigm|2^kx+1,
\end{align*}
where $\gcd(2^kx-1,2^kx+1)=1$. Then $\gcd(y-x,y+x)=1$ so $y^2-x^2\bigm|2^ky-1$. We clearly have $2^k-1\bigm|y-1$. By $(1)$, $x=1$ and $y=2^k$. Then $m=1$ and the two positive divisors were $2^k-1$ and $2^k+1$.
 A: Too long to comment:
It is necessary that 
$$y=\left\lfloor 1+\frac{x-1}{2^k-1}\right\rfloor(2^k-1)+1$$
Proof : 
We can write
$$y-1=m(2^k-1)\tag1$$
where $m$ is a positive integer.
Also, $$y^2-x^2\mid 2^ky-1$$
implies $$2^ky-1-(y^2-x^2)\ge 0\tag2$$
From $(1)(2)$, we get
$$2^k(m2^k-m+1)-1-(m2^k-m+1)^2+x^2\ge 0,$$
i.e.
$$(2^k-1)^2m^2-2(2^k-1)(2^{k-1}-1)m-(2^k-2+x^2)\color{red}{\le} 0,$$
i.e.
$$\small\frac{2^{k-1}-1-\sqrt{(2^{k-1}-1)^2+2^k-2+x^2}}{2^k-1}\le m\le \frac{2^{k-1}-1+\sqrt{(2^{k-1}-1)^2+2^k-2+x^2}}{2^k-1}\tag3$$
Since we have
$$\frac{2^{k-1}-1+\sqrt{(2^{k-1}-1)^2+2^k-2+x^2}}{2^k-1}\le \frac{2^{k-1}-1+(2^{k-1}-1+x)}{2^k-1}\tag4$$
and
$$x\lt y=m2^k-m+1\implies \frac{x-1}{2^k-1}\lt m\tag5$$
it follows from $(3)(4)(5)$ that
$$\frac{x-1}{2^k-1}\lt m\le 1+\frac{x-1}{2^k-1}$$
from which
$$m=\left\lfloor 1+\frac{x-1}{2^k-1}\right\rfloor$$
follows.$\quad\blacksquare$
A: Let $y = 1 + (2^k - 1) i$ and $2^k y = 1 + (y^2 - x^2) j$.
Then
1) $2^k y - 1 = (2^k-1) (2^k i+1) = (y^2 - x^2) j$,
2) $(y-1) (y+i) = i j (y^2 - x^2)$,
3) $(-(2^k-1) + j (y^2 - x^2)) ((2^k i+1) + j (y^2 - x^2)) = 
 i j (y^2 - x^2) 2^{2k}$,
4) $(2y(i j-1)-(i-1))^2 - (i j-1) i j (2x)^2 = (i - 1)^2 - 4 (i j-1) i$,$\quad$ aka Pell equation,
5) $(j (y - x) - 2^{k - 1}) (j (y + x) - 2^{k - 1}) = 2^{2 (k - 1)} - j$,
6) $(2^k-1) (-(2^k i+1) + (2 + (2^k-1) i) i j) = (x^2 - 1) j$.
gp-code for verifing 5) (actually computable for $2\le k<48)$ :
ijk()=
{
 for(k=2,1000, for(i=1,k,
  m=2^k-1;
  yo=1+m*i;
  J=divisors(m*(2^k*i+1));
  for(q=2,#J-1,
   j=J[q];
   z=2^(2*(k-1))-j;
   D=divisors(z);
   for(l=2,#D-1,
    u=D[l]; v=z/u;
    s=u+2^(k-1); t=v+2^(k-1);
    if(s!=t,
     if(s%j==0&&t%j==0,
      y=(s+t)/2; x=abs(s-t)/2;
      if(y==yo,
       print(yo"    "k"    "i"    "j"    "s"    "t"    "x,"    "y)
      )
     )
    )
   )
  )
 ))
};

Code for 4) (evaluate over numbers $d=ij-1$):
ijd()=
{
 for(d=3, 10^6,
  IJ= divisors(d+1);
  for(l=1, #IJ,
   i= IJ[l]; j= (d+1)/i;
   D= d*i*j;
   if(!issquare(D),
    C= (i-1)^2-4*d*i;
    Q= bnfinit('X^2-D, 1);
    if(bnfcertify(Q),
     fu= Q.fu[1]; \\print(fu);
     N= bnfisintnorm(Q, C);
     for(v=1, #N, n= N[v];
      for(u=0, 100,
       s= lift(n*fu^u);
       X= abs(polcoeff(s, 0)); Y= abs(polcoeff(s, 1));  
       if(Y, if(X^2-D*Y^2==C, if(X==floor(X)&&Y==floor(Y), \\print("(X,Y) = ("X", "Y")");
        if(Y%2==0,
         x= Y/2;
         if((X+i-1)%(2*d)==0,
          y= (X+i-1)/(2*d); \\print("(x,y) = ("x", "y")");
          if((y-1)%i==0,
           k= ispower((y-1)/i+1, , &t),
           if(k&&t==2,
            if(2^k*y==1+(y^2-x^2)*j,
             print("    i= "i"    j= "j"    k= "k"    (x,y)= ("x", "y")")
            )
           )
          )
         )
        )
       )))
      )
     )
    )
   )
  )
 )
};

A: COMMENT.-We have $$2^ky-1=a(y^2-x^2)\\y-1=b(2^k-1)$$ where the given solution gives the identities $2^{2k}=2^{2k}$ and the equivalent $2^k=2^k$, not properly a system of two independent equations.
Suppose now a true (independent) system
The first equation gives a quadratic in $y$
$$ay^2+(-2^k)y+(-ax^2+1)=0$$ and the difference of the two equations gives another quadratic
$$ay^2+(2^k-1)y+(b-ax^2-b2^k)=0$$ Assuming these two quadratics have both roots $y$ equal we finish because the coefficients should be proportional and the first ones are equal ($a=a$) so the absurde with the seconds coefficients. Then there are not a true system.
Missing the case in which the two quadratics have only one common root. A known necessary condition of compatibility for this is
$$(ac'-a'c)^2=(ab'-a'b)(bc'-b'c)$$ when the quadratics are $$ax^2+bx+c=0\\a'x^2+b'x+c'=0$$
A: I've finally solved it!
My solution to this question proves a generalized version.
To deduce this special case, set $z=2^k$, note that $z$ is divisible by $4$, and use Theorem 9 to conclude that $y=z$ and $yz-1=y^2-x^2$.
Then $y=2^k$ and $x=1$ as desired.
