Long VI names should not be a problem when downloading through the "Operate -> Download Application" or the "Run" button in the LabVIEW development system. It is only the file system on the controller that does not support long filenames, where the above processes download the VI to RAM, not to the disk.
The most likely causes for these errors on a FP-2000 would be:
1. Mismatched firmware and FieldPoint Explorer versions. If your FP-2000 has LabVIEW 6.1.1 on it, you must install the upgrade to FieldPoint Explorer 3.0.2. Conversely, if your FP-2000 has LabVIEW 6.1.0 on it and you have FieldPoint Explorer 3.0.2 installed on your Windows computer, you must upgrade the FP-2000 to LabVIEW 6.1.1. Note that the 6.1.1 version number only applies to the firmware
on the FP-2000 module. Your LabVIEW development system will always remain at version 6.1.
2. If your VI is particularly large, your FP-2000 may be running out of RAM during the download process. An easy way to test this would be, write down the name of one of the VIs that fails to download. "FP (Close).vi" for example. Power cycle your FP-2000, then target it and open that VI by itself. Attempt to download this VI. If you get the same error, then likely this small VI is not encountering a memory problem, but you are in fact running into the issue mentioned in #1.