library settings

What about explicitly adding the file/s? The libraries are only places for Quartus to look for design files that match the missing component name. For example, if your HDL instantiates a module/entity called blaa, Quartus will first look through all the files specificially added in Project -> Add Files to see if blaa is defined anywhere. If not, then it looks in the libraries for files that have that in the name, like blaa.v or blaa.vhd. It does not search all files, just known filetypes. It also won't look inside the files if the names don't match, so if you have a file called blaa_altera.v, which has a module called blaa inside, it won't look at that because the name doesn't match blaa. Just some ideas as to what might be happening.

It is much easily to explicity included your source. QSYS should have creted .qip file that you can add to the file list nd it should add all the generated HDL files.

First of all, Thank you for your reply, Rysc and Tricky.

If it's a QSYS file, then letting the .qip handle it is the way to go. If it's explicitly pointing to the file, there should be a warning that it wasn't found or something like that. If it is found, it should say what modules it found in the file. I'm really not sure what's going on though.

.qsys files are not used in Quartus, it only uses the generated HDL files. So remove the .qsys file from the file list. Is this missing component a custom one? what language is it written in? if its VHDL - have you used a component declaration, and does that declaration match the entity declaration? (a missmatch will cause an error like the one you suggest).

Here's an update of my issue.