With a client we had a problem. His theme has a dark header, so his logo was white. He added the logo url in the WHMCS configuration.
The problem then is that the online invoice has a light background, and the logo was barely visible.
We then decided to create a different logo. For the PDF invoice the problem is easily solved. All you have to do is to upload the you logo here
as a png or jpg file. Even if you want to use your regular logo you need to change this file here, otherwise WHMCS will show a placeholder in your pdf invoices. So for the PDF invoice all you have to do is to upload a logo in different colors here.
If you also want you can get our hook and change the logo on the online invoice as well, without the need to edit the template, just editing a setting in our Custom module to manage hooks settings and uploading this hook.