Current beer to harvest culture from is Flanders Red. It was fermented with Gigayeast sour cherry funk in primary then racked to a carboy at ~1014SG. My plan was to ferment one or two more batches of Flanders red with neutral ale yeast then add culture from previous batch to the secondary.
I am not overly concerned if there is a bit of drift over time as long it produces a pleasant flavour profile. From my studies I understand that many commercial brewers manage their fermentation like this as it is not viable to make a new culture for each batch.
The decision to ferment clean then add brett/bacteria to secondary, or primary only using the gigayeast culture is going to depend on your preference. Does the current beer need more or less funk/sour, or is it perfect?
The former technique will leave less sugars for the brett/bacteria, and will likely result in a less funky/sour beer (although that is not a guarantee). The latter technique will likely lead to a funkier, more sour beer. However, I'm a bit worried about the amount of viable sacch/brett/lacto in your carboy. If you've already tossed the yeast cake from primary, you'll likely not have much at the bottom of your fermentor. The other consideration is that sacch fades quickly over time. After 3-4 months, you have a lot less viable yeast. If you're pitching onto an entire yeast cake, you'll be fine, but if the yeast cake from primary is gone, you'll want to add sacch.
My recommendation is:
1) If the beer tastes perfect to you now, add fresh wort to the empty carboy after you bottle the contents. Co-pitch with a sacch yeast. This will allow the brett/bacteria to get some of those simple sugars before the sacch eats them all.
2) If the current beer is too sour/funky. Do exactly what you were planning- add brett/bacteria to secondary.
3) If you want more funk, I would take the dregs of the carboy and put them on a stir plate with 1-2l of wort, then use this as a starter for your next batch. This should give you a higher proportion of active brett/bacteria compared to the other options.
.....and yes, I do realize I'm sort of ignoring sacch/brett interactions, which can cause all sorts of funky flavors. However, because we don't know the exact combinations of sacch and brett, it's a bit hard to predict these a priori.....