Quartus source control

Check the "Analysis & Synthesis Source Files Read" table in the compilation report to make sure you haven't overlooked any source files.

If you are using incremental compilation and want to reproduce your results without going through the same complete sequence of incremental compiles again, then you need the db directory. (Actually, you need only certain files in that directory, but Altera doesn't document which ones. To be sure you have everything you need, you have to keep the whole thing.)

You listed Name.out.sdc, which makes me think you are using write_sdc. That command is OK to create your initial .sdc file, but never use that command again after the file exists. It always creates a new file from scratch with its own file organization. Anything you've done to rearrange lines or add comments will be lost. write_sdc can change the file in other ways too as controlled by the -expand argument.

You said that the "simulator seems to work without [the \simulation\*.*] folder". You need to keep the simulation folder to do a gate-level simulation unless you regenerate the .vo/.vho/.sdo.