Thanks For the comment,

All Gnuastro programs only keep essential keywords in their output, it is not just Warp. But there is a simple solution to this issue that is described below.

Let me first explain the reason for this behavior: we usually need more than one program to complete a task and moving around all the non-essential keywords in between intermediate data products is just an extra overhead and can cause conflicts.

This overhead can be significant because in the FITS standard, the keywords are kept in blocks of 2880 bytes at the start of the file (which translates to 36 lines of 80 bytes: the length of each keyword). When you initially define the output array in CFITSIO there is only one of these blocks for keywords. As you add more keywords such that a new block will be necessary, CFITSIO is forced to shift the whole data array also (because these blocks should be at the start of the file). This shift can slow-down the write operation on larger images.

Furthermore, searching for keywords that are not affected by the operation of each program will also add a lot of overhead. Especially as the number of keywords increase to very large number of keywords (I have seen files with thousands of keywords).

Preserving all extra keywords can also potentially add many bugs/annoyances for:

• Users who may have keywords that are meaningful for any program (making them worry about loosing information).
• Developers, who will have to keep track of the keywords that are created during the operation of a program (sometimes they are not known a-priori: they depend on the processing). 

All this complexity is really against the Unix philosophy; which has a term explicitly saying: "Don't clutter output with extraneous information".

Since the Job of the Warp program is to only Warp the pixel grid, any keyword that is not directly related to the pixel grid is "extraneous". 

The solution however is simple (again following the Unix philosopy: "Make each program do one thing well. To do a new job, build afresh rather than complicate old programs by adding new 'features'."):

Gnuastro has the 'astfits' program which you can use (through its '--copykeys' option) to copy keywords from one file to your final output (possibly after many operations through any number of programs).

Here is an example following your original example (just replace 'KEY1', 'KEY2', 'KEY3' with the keywords you want in the end).

$ astwarp --hdu=1 --rotate=0 -o warped.fits original.fits

$ astfits original.fits --copykeys=KEY1,KEY2,KEY3 \
          --output=warped.fits --outhdu=1

You can even add a "title" key entry for the new keywords you want to preserve in the final output (of many operations) through the '--write' option of 'astfits' like below.

$ astwarp --hdu=1 --rotate=0 -o warped.fits original.fits

$ astfits warped.fits --write=/,"Pipeline keywords"

$ astfits original.fits --copykeys=KEY1,KEY2,KEY3 \
          --output=warped.fits --outhdu=1

You can curate the keywords in your final output from many separate files and in any order and any grouping (with different titles) to be more clear for the final recipients of your pipeline's data products.

For more on the keyword editing features of the 'astfits' program, see https://www.gnu.org/software/gnuastro/manual/html_node/Keyword-manipulation.html

I hope this helps clarify that this issue is not a bug, but a feature of Gnuastro ;-).

However, to avoid confusion for users that are not use to this behavior I am keeping this bug open to add all the discussion here inside the manual to be clear for the users.