I have been working slowly on this beach map and everything was going smoothly until last week.

1st problem: I tried to compile the map one day after doing a lot displacement with paint geometry. Now it won't compile. I keep getting the error "Allocated lightmap: lightmap too big to fit in page" So then I went here http://www.interlopers.net/errors/index.php?e=4-10 and used the tool that was provided. The tool allows all lightmaps to work it also created a new file and it compiled.

However it brought new problems. A lot of prop_physics that I had disapeared. Some trees, hedgehogs, etc. I also cannot seem to compile water now. I do not know if this is because of this tool or if because I displaced the area,(made the dunes on the beach) and this changes what or how I put props in.

Any ideas?

First off i am no expert but i have had the same problems with disappearing props. One thing i found is that if I put a prop_static inside another prop_static, the smaller prop would not compile. And by inside, i mean the redbox that props are seen as from a distance in hammer, (before they are rendered). Secondly try changing your disappearing props to dynamic. sometimes fixes disappearing keypads and trees for me. As far as displacements go its a crapshoot, and the interlopers link is at your own risk.  Also this may sound repetitive but you may be leaking. its vey easy to accidentally move something ecspecially in 2d views on complex maps and alot of times its almost impossible to spot the leak in the 3d view. hope that helps.