pstool using pdfcrop fails on complex document

Following a proposal here Proper toolchain for pdfLaTeX and psfrag including hyperref, I switched my pstool crop stage to pdfcrop to avoid a bug in preview. I compile a complex thesis document, distributed over several *.tex files.

Now the pdfLaTeX run fails on converting the *.eps files to *.pdf files whenever I cause a new conversion of an *.eps image without(!) cleaning the project in advance, deleting all temporary files. Specifically, the error

! File ended while scanning use of @writefile.
<inserted text> 
                par 
l.1772 ...always_the_chapter_with_the_changed_image.aux}
                                                
?

occurs in the *.tex file that contains the image to be converted. This can be reproduced for all images in all chapters.

I found one possible hint: The file …always_the_chapter_with_the_changed_image.aux has a structure like

relax
providecommandhyper@newdestlabel[2]{}
@writefile{toc}{defcounter {refsection}{0}relax }@writefile{toc}{contentsline {chapter}{numberline {6}Implementierung einer digitalen Werkzeugkette}{177}{chapter.6}protected@file@percent }
@writefile{lof}{defcounter {refsection}{0}relax }@writefile{lof}{addvspace {10p@ }}
@writefile{lot}{defcounter {refsection}{0}relax }@writefile{lot}{addvspace {10p@ }}
...
...
newlabel{fig:Nizam_Total@cref}{{[figure][3][6]6.3}{[1][182][]183}}
@writefile

ending with the @writefile line, while all other chapters continue in their *.aux files with a list like

setcounter{page}{79}
setcounter{equation}{0}
setcounter{enumi}{4}
setcounter{enumii}{0}
setcounter{enumiii}{0}
setcounter{enumiv}{0}
setcounter{footnote}{0}
setcounter{mpfootnote}{0}
setcounter{part}{0}

which is missing for the chapter containing the changed *.eps image.

In order to prepare a minimum example, I tried to find a minimum project complexity to reproduce the error, but it is not easy. Sometimes, simply removing normal text led to a normal compilation. But also a plain large document of repeated text compiles well. So I assume it is somehow related to document complexity.

Note, when I clean all temporary files in advance, the document compiles well!

Can you advise me how to track the issue? As I told, my techniques failed to provide a proper minimum example…