split database MDE backend?

Ive worked in Access for a few years now (self taught) and have deployed a number of databases containing an MDE front end and single back end of tables which ive always left as an MDB file.

Im now getting a "Microsoft Access Was Unable to Create an MDE Database" on one of them when creating an update for the front end. Ive had this before and its been down to corruption however when Ive done a bit digging I found a reference from Microsoft stating the error can be caused when you have a link to an MDB database (which obviously this one does).

Ive never thought before about compiling the back end and am happy to do this but one thing thats bugging me is, what if I have to make updates to the table strucutre? for the front end its easy, I have a development (MDB) version which gets updated and reissued as and when. On the back end version however I couldnt do this as the data would be out of date.

How does everyone else get round this? is it simply a case of running with the MDE and if you need amend the structure, copying all the tables to a new MDB file, changing and then recreating the MDE?