It sounds like you are 'just' now diving into having a company standard template and your company has been working (for some time) on a project by project basis, with attributes being different on most of them.
Unfortunately there is no 'quick fix' for this, in my experience.
Speaking from personal experience, our company did not have a proper template before we got to about ArchiCAD11 I would say, giving us a back log of projects from version 7 to 10 that were just a mess of attributes. We decided to make a clean cut and not re-use old content from the new template onwards and rather recreate things so they can be used cleanly in the new project to come. We also based our template off the standard template for our local version to keep updates simple.
Now sometimes our reseller will rename attributes in their template for version updates or change things, and I curse at them silently, but for the most part updates have been relatively pain free.
By coincidence I've recently had to revisit two very old projects and it took me about a day or day and a half of work to get them working in the latest archicad with our current template settings (this includes going through library parts and replacing them with the new library, which doesn't happen automatically with libraries that far back).
My process has been:
1. delete all unneeded views, hidden layers etc
2. purge all unused attributes
3. copy by index and then append the highest index number attribute from our latest template (thus creating a suitable high number that does not exist)
4. copy the remaining attributes to the right (untitled.aat window) with append
6. rename those copies with a !! in front
7. append these back to the left, leaving them with very high index numbers
8. go in to the respective attributes main settings window (layer manager, fill, linetype etc) and one by one delete and replace them with the copies
Make sure you fix fills and surfaces before going on to building materials.
When all is done, go to attribute manager and import your template to project by index. Now you go through your old copy attributes again and delete them to be replaced with the template attributes that fits them most.
This sounds like a lot of work, but unless your old project had absolutely no current template to begin with (in other words someone created every single attribute from scratch), you will find that there are a lot of layers and fills and line types and surfaces that already have a similar attribute in your new template, only with slightly different name or settings so you can just replace them in the final step of replacing attributes by index from the template.
Some slightly related 'best practice tip' that is pretty much a rule in our office: if you find yourself with a fill or a surface or something that is almost what you need, but needs one minor change: still create a copy of that attribute and give it a new name. This means you can mostly copy things between projects without problem.
Erwin Edel, Project Lead, Leloup Architectenwww.leloup.nl
ArchiCAD 9-26NED FULL
Windows 10 Pro
Adobe Design Premium CS5