I have two projects I need to do but it is mandatory to use a custom Bootstrap CDN in the template they provide (government use). It is also based on Bootstrap 3.3.6 …
Will I still be able to use Wappler?
What obstacles will I face?
I would really hate to have to go update all my DW extensions. 
In my experience they like nicely commented code. It may be audited for compliance so ask them for contact details for their compliance officer if they have one, and run everything by them as necessary (also, more modern departments may have private GitHub repositories you may want access to). Some departments are more strict but in general I found most of the old DW code base to be acceptable for internal use. Can be a lot stricter for public domains though! Usually they will inform you of what is acceptable and what they don’t like to see. You will be amazed how the architecture changes across various departments. A lot of archaic services still live. The last job I did within that realm was hosted on a W2K box running unpatched IIS (remember Code Red?)… 
The back-end on this box was powered by Access!
The horror!
Apparently I will have to go back to DW and update all my DMXZone extensions for these projects. Page won’t even render in design view.