altered STL in meshlab, now Lychee keeps filling in areas I don't want

[Richard Andrew]

Hello. I bought a nice STL of the Black Pearl from Pirates-Carribean. I wanted to change it to reflect Blackbeard's ship. (Queen Anne's revenge) Queen Anne's had more cannons. so, I duplicated some of the cannon ports. I started with the original file which is just one portion of the hull. . ( see file Original) Then I cut out a port and saved it as it's own stl. Then I made holes in the original where 2 new ports would be added. Finally I added the ports and flattened the layers. I ran the flattened layers through a bunch of the "cleaning and repairing" commands in meshlab, as well as a bunch of the Manifold repair commands and Remeshing (close holes, etc.) some of the commands I repeated several times. . I will admit, I don't know the system well enough to know exactly what I am doing wrong. When I put it in Lychee, it tells me I have holes. When it "repairs" the part, it now has filled in some of the port openings I had made. I have tried every configuration of repair I can think of, and I keep having the same trouble. It is possible that the file is fixed enough, and I MIGHT be able to print it without Lychee repairing the file. Does anyone have any suggestions? Most of the commands are multi-syllabic unknowns to me. I am not trained in the program, but it often works out sufficient for what I want to do. I would appreciate help By the way, when I tried saving the "fixed" file from lychee back to meshlab, I got a mess. (see "mess)