By ‘COVID-19 CLC’ guidelines, I assume you are referring to the CLC ‘Site Operating Procedures’ document, with version 3 issued on 14 April.
From your reference to CDM Regulations 2015, I am assuming that the Contractor has been appointed as Principal Contractor, so is required under s13 (4) © to provide welfare facilities in accordance with Schedule 2. These facilities are not prescriptive, being described as ‘suitable and sufficient’, presumably so as not to place any limitation or restriction on what is to be provided, which should be based on an assessment of particular risks and circumstances.
Although the ‘Site Operating Procedures’ offer sensible guidance on the practical issues involved with following Public Health England’s guidance, one of the issues is that the requirement for social distancing, that is to maintain 2m between persons, is instructed as guidance in England, unlike in Wales where the requirement was introduced under amended Regulations on 03 April 2020. There are restrictions on movement and gatherings, although this is not the same and there has been some confusion on police powers and what they are actually required to enforce.
Although not mandatory in England, however, a key obligation under CDM Regulations 2015 is that the Principal Contractor is obliged to ensure that a construction site must be, so far as is reasonably practicable, made and kept safe for, and without risks to, the health of a person at work there’ (Part 4 s17 (2)). This requirement must extend to accounting for any matter which could affect the health of persons working on Site, including the risk of being infected from a virus. Consequently the measures detailed in the ‘Site Operating Procedures’ guidance seem sensible in complying with this requirement.
Applying the contract, if the Works Information is prescriptive in the requirement for Welfare facilities, then any such revisions would change this, but whether this would be a Contractor proposal or a PM’s instruction would depend upon how the ‘Site Operating Procedures’ are adopted, including any instruction given by the PM under clause 19.1. Essentially who is responsible for making the change and whether it is a contractual or a health and safety issue.
It may be that, under the circumstances, the contract has been varied, such as a Deed of Variation, possibly in line with the model form issued by the Cabinet Office as part of the revised Guidance Notes associated with Procurement Policy Note 02/20, dated 06 April 2020.
Whatever the situation I would hope both parties have engaged in dialogue to address the matter sensibly, although I appreciate that is not always the case.