fix prepare message for RFE

[IAlibay]

Fixes prepare message for RFE and AFE Protocols.

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.32%. Comparing base (41f1684) to head (9938cbb).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_afe/base_afe_units.py	66.66%	2 Missing ⚠️
src/openfe/protocols/openmm_rfe/hybridtop_units.py	66.66%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1915      +/-   ##
==========================================
- Coverage   94.99%   91.32%   -3.68%     
==========================================
  Files         206      206              
  Lines       18287    18296       +9     
==========================================
- Hits        17371    16708     -663     
- Misses        916     1588     +672     

Flag	Coverage Δ
fast-tests	91.32% <66.66%> (?)
slow-tests	?

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[jthorton]

LGTM!

[hannahbaumann]

Thanks @IAlibay ! Just the one comment, otherwise lgtm!

[github-actions]

No API break detected ✅