Don't lose heart and write it off. RAeS accreditation is as respected as IMechE, it just follows a different set of guidelines for course content to achieve accreditation by the relevant institution. Accreditation means the course is of a high standard and is suitable as a pre-requisite for Chartered Engineer status.
I would definitely speak to the HR department first and explain your concern. Ask them to follow this up with a confirmation e-mail. This shows you are pro-active, can communicate effectively and are methodical and determined. All qualities they will be seeking and is a good opportunity to get yourself known ahead of others.
This alone may be enough to secure an interview with the HR department in the first instance.
Make sure you have all of the relevant information to hand BEFORE you call them. i.e. job title and reference number, full university course title and reference code, list of course content, name of your university sponsor / references and their contact details etc.
Plan what you are going to say and make a list of all questions you need answers for. Make a note of who you spoke to, their position in the company and their contact details. Don't forget to thank them afterwards.
Employers want to know if the course is accredited because:
a) Degrees are awarded by university, not by a national body like say GCSE's or A-levels. This is because the course content can and is so diverse - especially in the second and third years. Accreditation by the Engineering Council gives an extra layer of assurance that the content and academic standards of any given course, meet a recognised international standard. Not all universities and degrees are the same.
b) Larger companies will have systems and procedures/training in place for you to achieve Chartered Engineer (CEng) status within typically 4-6 years. This follows periods in a diverse range of departments including: R&D, production, testing, project management, sales, finance, health and safety, etc. It also means you are mentored throughout your training and have demonstrated responsibility for other staff and decision making above the level of technician.
Good luck, do not give up. Engineering degrees are very desireable.
Do let us know how you get on.