fixing missing links between files

After doing what seemed like the same steps (deleting and recreating bsfs and bdfs, setting project top, removing and re-adding files, cursing...) over a few times, I was able to get by the previous issue. All I can figure is some file must have been out-of-date.

More mysteries awaiting solutions:

I have been working with a project that has two parts; the nios part of the project sits in the main project folder along with its bdf and associated files. One of the symbols on this top bdf refers to a large chunk of logic whose files I keep in a sub-folder (including its own bsf and bdf). I don't want to just plop these files all in the main folder. Quartus does not like this at all, and will only compile successfully if I delete the db folder before every compile (sometimes not even then).

In the project settings->files I have tried:

1 Just including the files in the main folder

2 Explicitly including all the files in both the main and sub folder

3 Doing# 1 and also the bdf in the sub-folder

4 Including the sub-folder as a library name only (is this correct?)

Although each one of these methods can work at times, it is not foolproof.

Option# 4 has been the most reliable as long as I delete the db folder every-single-time.

If there is a way to avoid this annoyance I'd love to hear it.

Another mystery behavior:

A compile that normally takes 30min will complete 'successfully' in 2min, yet only use 1% resources. How can it be successful if it has ignored most of the design?

Here I found I had to go back into SOPC and re-generate the system. I had not made any changes in SOPC, but I had been walking thru the SOPC dialogs to check settings. This seems to be enough to corrupt the database and require re-generation. As long as I know about this behavior I can live with it.

Another mystery:

SOPC shows a small red triangle next to one of my component base addresses. Why?

Another mystery:

The hierarchy tab for my project was not expandable. Once again this is the I-don't-see-your-project-files problem. I had to delete all the files in settings->files and re-add them.

Another mystery:

Adding all the project files in settings->files will lead to a compile error "file pllpll.....bb.v declared/included more than once...". This is a file(s) created by the pll wizard but I have to remove it from my project files settings. Is this normal? Why is it created if it shouldn't be used?