There are strict regulations with regards to bat conservation that you need to be aware of prior to starting any project of this nature. The Scottish Government Rural Affairs Department can grant what is known as a Habitat Regulation Licence. This will allow you to carry out the work subject to certain conditions. For more detailed advice on this subject, please contact NatureScot or the Bat Conservation Trust.
You must not go ahead and carry out the work without consulting the aforementioned organisations as you will be committing a criminal offence and will be liable for a large fine.