Isolating two bodies completely in space and understanding change in their mass due to change in potential energy When nucleons are isolated from nuclei, mass deffect can be seen easily. Similarly if we seperate two masses kept close to each other, to infinite distance, will their masses increase?
 A: Short answer:

[W]ill their masses increase?

No. But the mass of the system will.1
Not so short version:
The thing you may be missing is that the mass of a system is not the sum of the mass of the parts.2
When we say that a nucleus is less massive than the sum of the masses of the nucleons that went into it we don't mean that the nucleons got lighter. We do mean that the system's mass is less than the sum of the component masses because there is a negative contribution from their interactions with each other (a negative potential energy).
How does that work?
You find the mass of an object in relativity by measuring it's energy $E$ and it's momentum $\vec{p}$ in any frame, then computing
$$ m = \frac{\sqrt{E^2 - (\vec{p}c)^2}}{c^2} \;.$$
(In the object's rest frame momentum will be zero and this coincides with the equation everyone remembers.)
To find the mass of a system you add up the energies and momenta of all the parts,
\begin{align}
E_\text{tot} = \sum_i E_i \\
\vec{p}_\text{tot} = \sum_i \vec{p}_i
\end{align}
(where $i$ is taken over all objects and all fields3) and then compute
$$ m_\text{tot} = \frac{\sqrt{E_\text{tot}^2 - (\vec{p}_\text{tot}c)^2}}{c^2} \;.$$
The result is that in general neither summing the invariant mass 
$$ m_\text{tot} = \sum_i m_i  \;, \tag{uh uh!}$$
nor summing the "realtivistic mass"
$$ m_\text{tot} = \sum_i \gamma_i m_i  \;, \tag{nope!}$$
gives you the correct mass of the system (those each can be correct in specific situations).

1 I'm going to use the modern nomenclature in which "mass" (symbol $m$) means the invariant mass AKA the rest mass and there is no name or dedicated symbol for $\gamma m$ (the thing called "relativistic mass" in the older nomenclature).
2 While I don't like the 

"Let me list all the ways Einstein's physics differs from what you thought you knew ... Isn't that weird?" 

approach to teaching relativity I am always amazed by the failure of those lists to include this particular issue. Nor is this peculiar to using the modern nomenclature, even in the old nomenclature the rest mass of the system changes while the rest mass of each of the parts remains the same.
3 It is in the addition of the contributions from the fields that potential energies are taken into account.
