I think the DOS file format itself does not have an accurate way to represent vertical positions far above the level area top boundary, so there's a good chance your entrance might not work as expected even if it were played in the actual DOS game program. The behavior you see in Lemmix is arguably a bug (it's definitely a known issue as others have hit this before), the editor should not have let you move the entrance that far beyond the top boundary in the first place. After saving and reloading, Lemmix actually set the vertical position of the affected entrances to some really high value, resulting in them positioned far beyond the level area bottom boundary.
There is a way to get rid of the now wildly off-positioned entrances within Lemmix editor, but it's a little tricky:
1) in Lemmix zoom out a lot, at least enough for the entire level area to fit within one screen without scrolling.
2) make sure to turn on rendering of terrain, objects AND steel. That is, in the "View" menu, make sure "Terrain rendering", "object rendering" and "steel rendering" are all checkmarked.
3) Hold down Ctrl key, then use mouse to select a rectangular area (like how you select a rectangular area in a picture in, say, MS Paint) that covers the entire level area with margins to spare. The idea is to select every element that is at least partially visible in the level area.
4) Go to Edit menu and select "Copy".
5) Now hit the "A" key. It may not look like it did anything, but this is "select all" command, selecting every element in the level, including your "invisible" entrances.
6) Hit Delete key to basically remove everything in your level.
7) Go to Edit menu and select "Paste". This puts back everything selected during step 3, which should be everything in the level except the unwanted entrances.
Alternatively if you have LemEdit set up (requires DOSBox to run on most computers), there are easier ways to hunt down, select, and delete just the unwanted entrance objects with that editor.
