I'm not sure whether this problem is in tup itself or in libfuse3.

When I run tup on the minimal example whose files are attached below,
tup runs pdftex (correctly).  However, pdftex fails:

  $ tup init
  .tup repository initialized: .tup/db
  $ tup
  [ tup ] [0.028s] Scanning filesystem...
  [ tup ] [0.058s] Reading in new environment variables...
  [ tup ] [0.085s] Parsing Tupfiles...
   1) [0.002s] .
   0) [0.001s] auto
   [  ] 100%
  [ tup ] [0.098s] No files to delete.
  [ tup ] [0.098s] Generating .gitignore files...
  [ tup ] [0.141s] Executing Commands...
  * 0) pdftex test.tex
  This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdftex)
   restricted \write18 enabled.
  entering extended mode
  (./test.tex)
  *
  ! Emergency stop.
  <*>

  !  ==> Fatal error occurred, no output PDF file produced!
  Transcript written on test.log.
   *** tup messages ***
   *** Command ID=30 failed with return value 1
   [ ] 100%
   *** tup: 1 job failed.

I modified the tupfile to run pdftex under strace.  It showed that
pdftex read in the test.tex source file twice, the first time correctly.
However, on the second read-in, the file had zero size (which produced
the error in pdftex).  See the attached strace-extract.log