I can't imagine how this would create a problem and use the following logic..... Most lapping involves a "lap" which is a soft material (cast iron, brass, lead etc) and a "work".... In the process of lapping, the "lap" is charged (embedded) with an abrasive and then used to improve the surface finish of the "work".... During this process, all the embedding is in the "lap", not the work..... For a good overview of this process, see the attached link....
http://www.us-products.com/sitehtml/lapping.html
In the case of firelapping we use dead soft lead which we purposely embed with an abrasive.... We want the abrasive to embed in the dead soft lead to ensure that we get a consistent lap the entire length of the barrel.... Given the huge difference in hardness between dead soft lead and the barrel I can not imagine that any lapping compound becomes embedded in the barrel during the firelapping process.... This is also supported by the fact that MV typically increases by roughly 10% between a firelapped barrel and its base brethren.... Logically, if abrasives were embedded in the barrel then friction would result in a lower MV and not a higher one....
The only area you might want to think about is the brass used for the firelapping process..... Because brass is still significantly harder than the dead soft lead the abrasive should not transfer (embed) in the brass but it would be a higher risk than it embedding in the barrel....
Hope this helps.....