Firstly a comment. As laboratories that are already ISO 17025:2017 accredited do not typically seek ISO 9001 certification, I assume you are referring to the larger organisation going for ISO 9001 certification for support departments like HR and Finance ? A laboratory that is accredited to ISO 17025 conforms to the requirements of ISO 17025 clause 8, Management requirements for laboratory activities. As these are the clauses covered in ISO 9001 management, It is considered that the laboratory fulfils the intent of ISO 9001.
You can refer to a similar question and reply, Are there any things in ISO 9001 not covered by ISO 17025? at https://community.advisera.com/topic/are-there-any-things-in-iso-9001-not-covered-by-iso-17025/
Is it better to integrate or have two separate manuals. The chances of having an integrated or combine audit is zero, since it is two separate bodies. There is a strong suggestion to integrate the manuals”
This is a organisational preference. If top management is the same for the ISO 17025 and ISO 9001 activities, then rather have one manual. This is simpler, and duplication will be avoided. The argument for two separate manuals can be made if there are different people involved, for different departments, such as HR. I suggest you look at the risks of combining them, versus having them separate in terms of responsibilities for processes such as dealing with complaints and noncomformances, auditing, management review and couemntation.
For more information, see ISO 17025 – Main guidelines at https://advisera.com/17025academy/what-is-iso-17025/ and the article ISO 17025 vs. ISO 9001 – Main differences and similarities at https://advisera.com/17025academy/blog/2019/07/11/iso-17025-vs-iso-9001-main-differences-and-similarities/ for some more insight.