I remember the developer of Vehicle Simulator told me that he used to use the “reset xform” modifier in 3ds Max to accomplish the task of getting everything oriented correctly. Would there be something similar in Blender?
Kind Regards
Skull Kid
I don’t think so, other than rotating everything at once to be the correct way round and then Applying rotations and scales to all selected meshes… You need to get rid of the scale -1 in X axis for your hull… (see your first post picture).
Cheers, Clock.
EDIT:
Backup your project FIRST!
Try with a simple mesh that is orientated Z up.
Ah, a lot has happened since then. Here’s the WIP, as of Mars 19, 2017. Strange thing is, if I apply the rotation to the rudder and propeller, the propeller rotates along Blender’s Z axis, and not along the Y axis. Same as for the rudder, and the animated doors at the bridge.
Go to Edit mode and rotate the vertices so it looks right again…
Without the model I am guessing - append the offending bits into a new blend file and post them here for me to dissect, without the images of course!
Cheers, Clock.
Did you rig it with bones or just keyframe Transforms? If you keyframed transforms, just move the keyframes to the correct axis.
The thing is, it exports correctly into Vehicle Simulator (this ship is meant to be a payware add-on for this simulator) but the program Thinks the ship is paper thin along the Blender Y axis… so it tends to “bounce” up and down a lot along Y axis.
Have you applied the scale? - try with just a simple mesh to start with - that will show you where the problem might lie. I have no knowledge of the simulator so can’t do any testing for you.
Cheers, Clock.
EDIT:
An X scale of -1 will/could make the programme think that the vertices are flipped along the Y Axis and cause issues.
I’m afraid I will have to give up on this… and use what I’ve used before. I’m sorry if I sound complex, but I’ve only slept 2 hours last night, so please forgive me if I sound a little strange 
Take a break - leave it a day or so then come back to it.
Take Care, Clock.
Hmm… strange… I exported the mesh as .obj, then imported it into Wings 3D, and from there exported to .x, and then it behaves just fine in Vehicle Simulator? Hmm…
EDIT: The DirectX exporter in Wings 3D is certainly not the fastest… takes… I don’t know… approximately 5 minutes to export it…
Yay! You have a solution it seems, but like me, at times, you don’t have a clue why… Pleased that you are many progress, keep me informed.
Cheers, Clock.
Hehe, I know what you mean… this ship was built ONLY in Blender 
But Wings 3D is a really nice piece of freeware as well, I may use it in the future for file conversion and such 
A NEW problem has appeared! Does someone here know how I can get rid of this sharp line that goes across the bow? It’s the solid railing that goes right there, but it’s not supposed to look like it’s been welded on, but it was simply a part of the hull.
It may or may not show up clearer in this shot. I want to eliminate this edge.
On holiday till next Wednesday, sorry no Mac, just my phone, I can look at it then. If nobody else has helped.
try SHIFT+E and key to 0.1 to smooth it, as a quick thought… or add an edge loop just below and scale it out a little…
Cheers, Clock
Hi again Clockmender!
Changing the creasing (Shift+E) doesn’t seem to change anything… hmm… this is quite strange… BUT I will continue to experiment with this little, “issue” or whatever I should call it
Happy Easter!
Kind Regards
Skull Kid
SOLVED! Now I can sleep well, without nightmares about this XD
Yes yes, the shading looks off, BUT the seam is gone. One step ahead, not backwards, at least 
Updates, and a new problem has arise! I need to move the back of the superstructure, BUT only a certain part of it 
The proportional editing doesn’t seem to work to achieve this. I basically want to move the back of the bridge wings (see image). I tried to use the Grease Pencil to draw out my problem in a OpenGL render (forgive my awful drawing skills, I am bad a drawing XD)
EDIT: I seem to have drawn the yellow line in the wrong direction, so I changed that.
I think I can achieve what I posted yesterday with a boolean cut, but it simply cuts away a huge hole in the superstructure, like below. I just want it to slice away a part of it, not cut right through it.
Below is the cutter, a cube object.
I solved by myself 
I scaled the back of the bridge wing accordingly to the normal Z of the back rail right at the back of the bridge wing, which gives this result:
Sorry I didn’t get back to you in time. The Boolean has removed the back faces - there are lots of tris (3 sided faces) in there that may also cause problems. I will do a quick mockup of how I would model this later today/tomorrow. Really you should stick with Quads (4 sided faces) for Blender - there are far fewer problems that way!
Cheers, Clock.