fixing missing links between files

[Altera_Forum]

Q7.2 web 

 How do I restore links between projects and files once everything is created? I am somehow losing the links between the bdf, the bsf it contains, and the underlying hdl for the bsf.  What I usu do is create a new project, then create a .v file and create a bsf for that file. Then I create a bdf and place the symbol on it, and make it the top level entity. I add the bdf and the .v file to the project in the file settings dialog.   Somewhere in this process links are lost since when I double click on the symbol, nothing happens. I can then remove the files from the project (settings dialog) and then do 'add all'. The link between the symbol and the .v file seems to be restored, yet when I compile I get 'Top partition does not contain any logic'.  What step is missing here?

[Altera_Forum]

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 All I can figure is some file must have been out-of-date.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?