I seem to have found my own answer through setting up a new dummy gae project and having a poke around, found that the 'Run As' > 'Run Configurations...' > '(x)= Arguments' > 'Program arguments' had an additional port defined prior to the rest of the argument beginning '--port=8888'. I removed the mention of '-codeServerPort 9997 ' and it now deploys to dev server and appears to be working as before.
eg
new dummy project: --port=8888 "C:\Users\tech1\SSD Storage\Eclipse Projects\workspace\dummy\war"
project that wouldn't deploy to dev server: -codeServerPort 9997 --port=8888 "C:\Users\tech1\SSD Storage\Eclipse Projects\workspace\test\war"