Maybe not.
If the samples are licensed for use in a certain application, it depends on how that license is worded and interpreted whether they could be used in another application. Ask yourself if the license would be violated if you were to "loan" your samples to a friend who then used them in an application for which you did not have a license. Most likely the licensor could successfully claim that your friend was infringing his copyright to the samples, and claim that he was using samples that were licensed to you as value added to your application's license without having a valid license himself. Probably you, or a court, would accept that interpretation. The same argument applies even in the case you describe, since your license for the second application is an agreement between you and the second licensor (Battery), it does not give you any more rights to use the samples you have licensed from the first licensor (Session Drummer) than it would give your friend. So the determining factor is whether your license for SD3 gives you unrestricted rights to the samples or restricts your use to the samples within SD3.
Most samples are licensed so that you can use the license to create music (otherwise what use would the samples be to you), but you cannot copy the samples and distribute them to others (otherwise the licensor has given you the ability to compete with him using his own property as your inventory). The fact that you are changing the format of the samples is not relevant, any more than distributing them on vinyl would be different than distributing them on magnetic tape. So is your use of licensed samples via another application to make your music (you are not distributing the samples themselves) within the terms of your SD3 license? That depends on the terms of the license and how it is interpreted. If there is any language indicating that you can only use them within SD3, you are probably out of compliance to use them in another application, if not then you may be able to do so under the assumption that your use is just an extension of the explicit or implied license to use them to make music, and the specific method (application) you use to do that does not matter.