I think it really depends on your buffer used for your IEX elution. I don't think a sizing column is sensitive to salt. If you still have concern with the salt from your IEX elution, just try changing the buffer to low salt when you concentrate your proteins.
should be fine. I do this all the time. I think unless your protein's oligomerization state is sensitive to salt concentration, otherwise salt concentration should not affect the purification. In fact I know some people actually using size exclusion column to do buffer exchange instead of dialysis when the sample volume are small.