That seemed to help but I eventually got another similar crash.

FWIW I managed to reduce (guix build graft) to just the code below, and
it’s enough to trigger a crash after a dozen of runs:

--8<---------------cut here---------------start------------->8---
(define-module (guix build graft)
  #:use-module (guix build utils)
  #:use-module (rnrs bytevectors)
  #:use-module (ice-9 vlist)
  #:use-module (ice-9 match)
  #:use-module (ice-9 threads)
  #:use-module (ice-9 binary-ports)
  #:use-module (ice-9 iconv)
  #:use-module (srfi srfi-1)   ; list library
  #:use-module (srfi srfi-26)  ; cut and cute
  #:export (replace-store-references
            rewrite-directory))

(define (exit-on-exception proc)
  "Return a procedure that wraps PROC so that 'primitive-exit' is called when
an exception is caught."
  (lambda (arg)
    (catch #t
      (lambda ()
        (proc arg))
      (const #t)
      (lambda (key . args)
        ;; Since ports are not thread-safe as of Guile 2.0, reopen stderr.
        (let ((port (fdopen 2 "w0")))
          (print-exception port #f key args)
          (display-backtrace (make-stack #t) port)
          (dynamic-call "abort" (dynamic-link))
          (sleep 1000)
          (primitive-exit 1))))))

(define* (rewrite-directory directory output mapping)
  (define prefix-len
    (string-length directory))

  (define (destination file)
    (string-append output (string-drop file prefix-len)))

  (define (rewrite-leaf file)
    (let (#;(stat (lstat file))
          (dest (destination file)))
      (catch 'foo
        (lambda ()
          (throw 'foo (dirname (string-append "/tmp/x" dest))))
        (lambda (key file)
          (call-with-output-string
            (lambda (output)
              (make-bytevector (expt 2 10) #x77)
              (string->bytevector file "UTF-8")
              (open-input-string file)
              (make-bytevector (expt 2 20) #x77)))))))

  (n-par-for-each (pk 'jobs (parallel-job-count))
                  (exit-on-exception rewrite-leaf)
                  (find-files directory (const #t)
                              #:directories? #t)))

;;; graft.scm ends here
--8<---------------cut here---------------end--------------->8---


Thoughts?  Whatever ideas you have could be helpful.  :-)

Cheers,
Ludo’.