I love libtool and it is great it is getting some additional Windows support.  Was happy to see the /Fe fix.  Unfortunately a biproduct of the newer MSVC support has caused a new issue in terms of the .exp files using with multi-step linking.

Libtool uses .exp files as input into cl.exe, and this works.  These are essentially just command line commands in a file and using the "@" arg.  An example is: https://github.com/mitchcapper/libtool/blob/baa1fe41f9a2697e2d5847c8e1c97996560d56d1/m4/libtool.m4#L5742 .  The problem though is .exp is also used by microsoft for their own export format:
https://learn.microsoft.com/en-us/cpp/build/reference/dot-exp-files-as-linker-input?view=msvc-140

So the first time through a make build it would succeed, when the .exp file is used.  The command though will override the input file itself as microsoft takes the output arg "-Fe$tool_output_objdir$soname"  and appends .exp for its export file and this is the same name libtool uses.   This causes the make to fail the second time with cl.exe complaining the file format is invalid (as it is now a binary file not the additional command line args).

I use libtool with several GNU projects I build: https://github.com/mitchcapper/WIN64LinuxBuild

and my libtool hacks: https://github.com/mitchcapper/WIN64LinuxBuild/blob/0c7a19c857c8feac3e258669512f0abdb99d59f9/helpers_gnu.sh#L141-L142 just mass replace .exp with .expsym I have a commit of this specific fix at: https://github.com/mitchcapper/libtool/compare/master...exp_extension_change

but I am not sure if this would be preferred for a patch.  As far as I am aware .exp is only used internally by libtool so this should be decently safe/not break anything.  Still you might prefer a windows only fix given MSVC is the only place this happens.  Let me know and I can update the commit and get it submitted. 

I read the process doc ( https://www.gnu.org/software/libtool/contribute.html#patches ) and understand I should be making a changelog entry and submitting it to the mailing list after posting it in this bug report.  I figured I would find out what direction was desired before creating the patch.