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It really depends on what is meant by converting to Java 2. If it means that your company will have an IBM Websphere Application Server and that all future application development will be on that platform, well then it ought to have no impact on your existing Domino applications. They will still run on your Domino servers.
On the other hand, if it means that all applications are to be converted to be native Java 2 applications, it would mean that you are going to port your applications to Java and move your data to an SQL server. It is highly unlikely that you are looking at this scenario, as it really is way too expensive to move all applicatons in a one-year timeframe.
The conversion might be that you are going to have something like IBM Lotus Workplace or the IBM Websphere Portal Server to be the company-wide launchpad for all applications. If you are looking at this scenario, your applications will be OK, but in order for them to be surfaced within such a portal (displayed in a window in the portal, maybe even allowing data to be manipulated from there), you are going to have to start using portlets. Some are freely available, but to service any custom-made applications with more than just data display, you will have to start coding your own Java-based portlets.
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