No audiable difference. Identical copies. You can prove this by doing a simple phase cancellation test between any plug in, in any format.
you may experience a delay shift with some audiosuite plug ins. Especially in plug ins that tend to use alot of CPU/processing. Double check the before and after to make sure you don't get a massive shift forward. You can also refer to the plug in manual for the samples information.
You can correct this easily by noting the samples used information on a track (with an active plug-in of that processor) and shifting it backwards then compiling a new track with the correction.
For example, if I want to process a group of tracks with a high quality plug in that takes up 19864 samples, I note that before hand. Then I simply go to shuffle mode, select a blank section before the waveform that I input as 19684 samples, delete and the shift is corrected. I'd compile that to obviously keep the new, time corrected file.