Hi Cyrus and thanks for your answer!
The client is using the base tag on all pages on the site, but with different URLs. For example:
Root page: <base href="http://domain.com/1.0.1.0/2/1/">
Subpage:
<base href="http://domain.com/1.0.1.0/5/1/"> OR
<base href="http://domain.com/1.0.1.0/13/1/">
Productpage:
<base href="http://domain.com/1.0.1.0/14/1/">
As you can se they are using a lot of different base locations and unfortunately we are unable to change the base URL and test.
We have problems with both broken links and rankings. Whenever a new version of the system is created, all base URLs will be changed. This may mean that old links are still there and will be broken.
What do you think Cyrus, can this hurt us from a SEO perspective? It must be confusing for Google with all the strange base URLs?
I think the best would be to rebuild the structure and remove the base tag!