What version of Flexi are you using? To an extent things will depend on what model Mimaki you are wanting up upgrade to. If for example a good used JV33 (or CJV) which are an order of magnitude easier to deal with than an older 4 head JV3 you would need to be running Flexi 8 or higher. While a JV33 is a discontinued model they are still fully supported and excellent machines if you find one in great condition. In excellent condition you can find one for 5 to 8k or so if you are patient and find the right one, sometimes even less (for a JV33-160, a -130 would go for even less). We have been running a JV33-160 for quite a long time now and I recently just added a second smaller one (JV33-130) that I picked up used so we could increase production. Had to replace the head and went ahead and replaced the dampers and the complete capping station and with the cost of the machine and parts I'm still under 4k in it in total. Faster, better print quality, and far less maintenance and fiddly than the old JV3 machines.
Now if you are looking at a current new model like a JV150 or JV300 you would probably need to have the very latest version of Flexi for one of those since those are really only about a year old. Otherwise you would have to try using Rasterlink and change everything about how you are used to running. We also use Flexi to drive our Mimaki's and Summa and its nice to not have to jump around between programs. Also the older SS2 Mimaki inks are near identical in gamut to the newer SS21 inks used in the JV33 and newer models so your older Flexi files will print darn near if not just the same in Flexi on the newer Mimaki. That's what I found years back when I upgraded from our old JV3 to a newer JV33. We were originally running Flexi 7 and had over time upgraded to version 8 prior to getting the JV33 and then upgraded to 8.6v2 and ran on that for a couple of years.