My main questions - are the delete face and move face commands able to be used regularly and create stable models?

More detail into why I am asking:

I have a complex multibody part (injection molded plastic part with overmold) that will fail if it regenerates. I am working on redoing the model to get rid of the features that were causing the failure - they were related to where several faces were deleted then a surface fill was created and knit back in to make the part solid again. The part has been tooled already so, I have to end up with the same geometry when I am done. The reason for the delete face: there were several small surfaces in an area that should have had only one. I am currently wondering if I am going to be forced down the same path again. Has anyone else struggled with delete facing causing model instability? Is the move face command stable? It might help me some for the current area I am struggling with. (This part curves in multiple directions and had to be drafted on the exterior prior to shelling.) Also, to save myself recreating sketches and such, I started from the old model and was trying to just correct the things that lead to the trouble spots. Should I just start over from scratch?

I'm currently on Soldiworks 2011 SP4.0, Windows XP x64.

This model was originally created in Solidworks 2007.

Thanks,

Carrie