Ok, I loaded up the merlin.oxp and purchased a ship and took a look at it. Looks just fine, everything is there.
BEFORE you do anything else make a copy of your custom "MandoMerlin-player.oxp" and move it somewhere OUTSIDE of your AddOns folder so you can start over if the changes you make don't work.
You say it seems as though it has been missing for awhile. Since you made your custom texture perhaps? In this oxp the merlin's subentities use the same texture map as the main ship. Because you probably want to have other merlins in the game you would have to do the following.
---add the prefix "mando" to all your subentities listed for the ship"MandoMerlin-player" in the key subentities.
<string>mandol-mexh 0.0 0.0 0.0 1 0 0 0 </string>
<string>mandor-mexh 0.0 0.0 0.0 1 0 0 0 </string>
<string>mandol-mpyl 0.0 0.0 0.0 1 0 0 0 </string>
<string>mandor-mpyl 0.0 0.0 0.0 1 0 0 0 </string>
<string>mandol-mwing 0.0 0.0 0.0 1 0 0 0 </string>
<string>mandor-mwing 0.0 0.0 0.0 1 0 0 0 </string>
---change the individual subentities in shipdata.plist by adding the prefix"mando" just as is below:
<key>mandol-mexh</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>3.5</real>
<key>max_energy</key>
<real>60</real>
<key>model</key>
<string>mandol-mexh.dat</string>
<key>name</key>
<string>mandol-mexh</string>
<key>roles</key>
<string>mandol-mexh</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>spawn: explosive_shrapnel 2</string>
<string>commsMessage: [engine-plea]</string>
</array>
</dict>
<key>mandor-mexh</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>3.5</real>
<key>max_energy</key>
<real>60</real>
<key>model</key>
<string>mandor-mexh.dat</string>
<key>name</key>
<string>mandor-mexh</string>
<key>roles</key>
<string>mandor-mexh</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>spawn: explosive_shrapnel 1</string>
<string>commsMessage: [engine-plea]</string>
</array>
</dict>
<key>mandol-mpyl</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>4.5</real>
<key>max_energy</key>
<real>60</real>
<key>model</key>
<string>mandol-mpyl.dat</string>
<key>name</key>
<string>mandol-mpyl</string>
<key>roles</key>
<string>mandol-mpyl</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>commsMessage: [pylon-plea]</string>
</array>
</dict>
<key>mandor-mpyl</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>4.5</real>
<key>max_energy</key>
<real>60</real>
<key>model</key>
<string>mandor-mpyl.dat</string>
<key>name</key>
<string>mandor-mpyl</string>
<key>roles</key>
<string>mandor-mpyl</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>commsMessage: [pylon-plea]</string>
</array>
</dict>
<key>mandol-mwing</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>2.5</real>
<key>max_energy</key>
<real>40</real>
<key>model</key>
<string>mandol-mwing.dat</string>
<key>name</key>
<string>mandol-mwing</string>
<key>roles</key>
<string>mandol-mwing</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>commsMessage: [wing-plea]</string>
</array>
</dict>
<key>mandor-mwing</key>
<dict>
<key>ai_type</key>
<string>nullAI.plist</string>
<key>energy_recharge_rate</key>
<real>2.5</real>
<key>max_energy</key>
<real>40</real>
<key>model</key>
<string>mandor-mwing.dat</string>
<key>name</key>
<string>mandor-mwing</string>
<key>roles</key>
<string>mandor-mwing</string>
<key>smooth</key>
<true/>
<key>death_actions</key>
<array>
<string>commsMessage: [wing-plea]</string>
</array>
</dict>
---change the model names for the subentities in the Models file by adding the prefix"mando". They must be exactly the same as the ones above.
---change the textures listed in the subentities' models so that they match the name of your ship's model's texture name(because the main ship and its subentities are supposed to use the same texture file.)
Your MandoMerlin-player is now completely independent of the merlin.oxp and the 2 should run perfectly together.
If you still have a problem seeing some of the subentities there are 2 possibilities:
--- the texture you created has missing texture parts so when the subent that is missing goes to read it it will have no texture for it and may be see through or white or other colors you don't want. I don't think this is the case but keep it in mind.
--- there is a problem for ships with subentities that disappear and won't show up, etc. in 1.75.2 and this is supposed to be fixed in 1.75.3 and this may be your main problem. However, I want you to fix and examine the rest of what I outlined above FIRST because this is what you should do anyway when you make a customized version of a ship.oxp with subentities so there is no conflict with the original ship.oxp when it is installed at the same time. After doing all this FIRST and the changes are working properly, then you can upgrade to 1.75.3 and handle that issue separately, ok?
Finally, just a reminder, before you do anything make a copy of your custom MandoMerlin-player.oxp and put it somewhere outside of your AddOns folder so that you can reload it if the modifications don't work and can try again. A good practice, you should always make a backup BEFORE changing something just in case it doesn't work.
It is a bit of work but this is just the sort of thing you need to do if you make your own custom version of a ship from an oxp. What needs renaming has to be renamed to prevent future conflict problems. Take your time, check for errors and all will be well.
Good luck with that and once again congratulations for getting this far. It will all be worth it when its done.