> Is there any way to tell LyX that the pdf-file exists and needs to be 
> copied to the temp-folder, so latex can find it?

I had a similar problem and have to thank the latest version LyX 2.0.1 for
solving the issue. This problem occurs when your figure (both .pdf_tex and .pdf)
in a directory (most commonly a subdirectory). To cut it short, let us assume
that the two files are in a subdirectory ./figures (I would recommend to always
use one such name for the directory for the reason to follow). Go to
Tools->Preferences->Paths->TEXTINPUTS prefix: by default the current document
directory is included (the dot .). Add the subdirectory path by appending
;./figures (the semicolon ; is to separate the two paths). I believe this should
solve such issues in he future except in the case that your subdirectoery has a
different name (e.g. ./img) in which case also append ;./img.



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