Let $A$ be a C*-algebra and $p,q \in A$ be projections. Assume there is an element $a\in A$ such that $\|aa^*-p\|<\frac{1}{4}$ and $\|a^*a-q\|<\frac{1}{4}$. Then there is a partial isometry $v$ with $vv^*=p$ and $v^*v=q$.
This is considered obvious in the paper I'm reading. I've tried to mimic the proof of the following proposition.
Let $p$, $q$ be projections in a C*-algebra A. If $\|p-q\|<1$ then p and q are unitarily equivalent.
Which involves using a suitable expression ($1-p-q+2pq$) and polar decomposition. But it's not going anywhere.
One can prove that $p,q$ are Murray -von-Neumann equivalent if they fulfill $$ \|aa^*-p\|<\frac 12,\quad \|a^*a-q\|<\frac 12. $$ The proof is standard (for example it is outlined in the comment of @ougao), I was just lucky to find $\|(1/2-p)^{-1}\|=2$.
We first assume that the $C^*$-algebra $A$ is unital.
First note that $(1-2p)^2=1$, hence $(1-2p)$ is its own inverse and $\|1-2p\|=1$. It follows that the inverse of $\frac 12-p$ is $2-4p$ and that $\|2-4p\|=2$. If $\|aa^*-p\|<\frac 12$, then $\|aa^*\|< \frac 32$ and $Spec(aa^*)\subset [0,\frac 32[\subset\Bbb{R}$. Moreover, since $\frac 12-p$ is invertible and $\|p-aa^*\|<\frac{1}{\|(\frac 12-p)^{-1}\|}$, we have that $\frac 12-p+p-aa^*=\frac 12-aa^*$ is invertible. This means that the spectrum of $aa^*$ has a gap at $\frac 12$, i.e., an open interval around $\frac 12$ which does not intersect $Spec(aa^*)$, since $Spec(aa^*)$ is closed.
Hence there exists an $r\in]0,\frac 12[$ such that $$ Spec(aa^*)\subset B_r(0)\cup B_r(1). $$ Similarly we find that $$ Spec(a^*a)\subset B_{r_1}(0)\cup B_{r_1}(1), $$ and we can assume that $r=r_1$.
We define on $D:=(B_{r}(0)\cup B_{r}(1))\cap\Bbb{R}$ the continuous function $$ f(x)=\left\{ \begin{array}{lr} 0& \text{if $x\in B_r(0)$}\\ 1/\sqrt{x}& \text{if $x\in B_r(1)$.} \end{array} \right. $$ Note that on $D$ the function $xf^2(x)$ is a projection with a distance less than $r$ to the identity function, i.e.,
$x^2f^4(x)=xf^2(x)$.
$|xf^2(x)-x|\le r$.
Then we apply functional calculus and set $v:= f(aa^*)a$. We have that $vv^*=aa^*f^2(aa^*)$ and moreover, by 1., $$ (vv^*)^2=(aa^*)^2f^4(aa^*)=aa^*f^2(aa^*). $$ Note that for any continuous function $f$ on $D$ we have $a^*f(aa^*)a=a^*af(a^*a)$ (this holds for polynomials and $f$ is the limit of polynomials).
Therefore we have $v^*v=a^*f^2(aa^*)a=a^*af^2(a^*a)$ and so, by 1., $$ (v^*v)^2=(a^*a)^2f^4(a^*a)=a^*af^2(a^*a). $$ So $vv^*$ and $v^*v$ are equivalent projections (they are the range projections of $aa^*$ and $a^*a$ respectively) and we compute $$ \|vv^*-p\|\le \|vv^*-aa^*\|+\|aa^*-p\|< r+\frac 12<1, $$ where $\|vv^*-aa^*\|\le r$ follows from 2.
Similarly $$ \|v^*v-q\|\le \|v^*v-a^*a\|+\|a^*a-q\|< r+\frac 12<1, $$ where $\|v^*v-a^*a\|\le r$ follows from 2.
Since $A$ is unital, there are unitary elements $u,s$ with $uvv^*u^*=p$ and $v^*v=sqs^*$. Then $(uvs)^*uvs=q$ and $uvs(uvs)^*=p$.
Finally we prove the general case. If $A$ is non-unital, embed it into its unitalization $A^\sim$, and there $p$ and $q$ are Murray-von-Neumann equivalent, i.e., there exists $b\in A^\sim$, such that $bb^*=p$ and $b^*b=q$. But then $b=pb$, since $\|(b-pb)(b-pb)^*\|=0$, and so, since $A$ is an ideal in $A^\sim$ we have that $b\in A$, hence $p,q$ are Murray-von-Neumann equivalent in $A$.