To keep a job around open it in the Production Manager and on the second tab select 'Hold" rather than "Delete".
As far as missing registration marks, how large a panel are your attempting and what is the firmware level in your plotter and what version of Flexi?
Graphtec/Flexi had a problem registering panels much more than 24-36" long. This started a massive finger pointing contest between Graphtec and SAI. Almost at the same time Graphtec released a firmware update and SAI release an updated to Flexi 7.6. Apparently one or both of these updates expanded the size of the are in which to search for registration marks. It mitigated the problem somewhat.
The problem is this inaccurate media feed on the printer, or much more rarely, on the plotter, or both. For the most part, trust the plotter, it's far more likely the printer.
For example, the printer thinks it's feed 10" of media but in fact it's only fed 9.9". This is fine for shorter panels but for longer work the error rapidly accumulates. In this example at 60" the error is .6" which is larger than the registration mark itself. Making the registration mark search are larger allows for a longer panel but doesn't really fix the problem. There will always exist an error accumulation sufficient to put the registration mark outside of the search area.
There's a setting in the printer's setup to compensate for media feed inaccuracies and a routine to generate a test print. The printer prints what it says is 10". You measure the print and enter what the length actually is. Unfortunately this varies wildly from media to media as well as the size and tension of the infeed roll. The best you can hope for is to come close most of the time.
SAI could easily mitigate this problem if they would simply publish the distances between the registration marks it automatically adds on contour cut jobs. Then you could manually register the print. But they don't and you can't.
If you suspect that some job or another isn't going to register properly, you can use manual registration marks. I do this on anything much larger than a couple of feet. If you're using manual marks, media feed inaccuracies will have absolutely no effect on registration mark detection. Using manual marks does an end run around Flexi's contour cut mechanism. You place your own marks on the print as well as a non-printing path that represents the contour cut. You don't use Flexi's contour cut at all. It takes a few times to get the hang of it but once you do it's not a big deal. There's a white paper available somewhere on Graphtec's web site that details the method.
