What does "lost a ship" really mean for a faction?

I think the whole concept hinges on what the definition of "a lot of money" is, in terms of the CDE universe.

We do get whole 600 Mc missions, but who is to say that that is that expensive in the grand scheme?.

If we look purely at stock designs, it seems that 50 Mc is pretty expensive, but if we look at player made designs, expensive could be only defined as above 5 Mc, for example. On the other end of the spectrum there's the people who make Yc ships.

Depends on how many qualified candidates are there.

Do mind that this is a setting after serious population drop - most of the pre-cataclysm human population didn't make it into space.
Also do mind, that it needs to justify pushing a newbie player out there to command forces despite being a n00b and making n00b mistakes.

Anyway, smaller is better, as it leaves room for interesting and suboptimal stuff to happen instead of just highly optimized laserstars zapping each other and incoming missile swarms at interplanetary distances. Even with built-in range limitations the combat between highly optimized vessels can easily get about as interesting and dynamic as watching paint dry, while micromissile swarms will bring any computer down to its knees and make its insides glow as brightly as radiators on [AE] reactors, so going small and imperfect (or murky enough due to political and other factors to justify variety of designs not focused on simply projecting maximum firepower at maximum range) works in gameplay's favour.

The background even implies that space combat is far from solved problem in the setting which excuses underpowered and often questionable stock designs.

There could be another possibility, instead of the cost, how long does it take to build a ship?

My personal opinion is that building a ship is too time-consuming and logistical-consuming to be done during wartime, such as during "Orbital Fallout"(J2249) it mentioned that the silo ship took years to build. And it was not until the final mission did we saw the completed Silo ship taking part in active combat(J2257).There was probably subcontractors off world and it would take lots of efforts to coordinate that even without occasional raids on commerce lines. Shipyards would conceivably take time to construct and their max size would be limited. A missing part could take months to rectify without the necessary tooling and material on hand , even if production time is neglected . Therefore, the cost might not have mattered as much as the time and availability.

If a ship takes years to build and the war is over in month, losing a ship is pretty devastating, not only that you have lost your strategical deterrent, you have no way of immediately replacing such a loss. If the war drags on them the problem became how to do war time ship building with enemy constantly sabotaging you.

I guess the fact that the player is installed as a commander has more thing to do with the fact that the player is the ?daughter? of the Martian president. During peacetime generals are nominated by their political skills and connections, and it could be that it was intended that the player act as a Commissar or a “政委” to his man and raise the general morale of the troop / make sure they are aligned. Perhaps it was felt that to nominate a captain from the crew would make for bad competition or that they would focus too much on saving their ship instead of devotion to completing strategical objectives. Either way it would appear that this is more a political situation than anything else. This scene was repeated when you have to evacuate a commander to Mars, who reveals that he/she is the relative of a Martian senator, showing that politics is everywhere in RFPN by the time war broke out.