By default, when you stop a Motion Sequence, the value will reset to "minimum" when Unipolar is selected and to "center" when Bipolar is selected.

You can either adjust the start point of the Filter Cutoff, or use MOTION SEQ HOLD instead of pressing MS STOP.

Option 1:
Set the start point for the Cutoff so it is open enough to play. Bipolar will allow you to move above and below the start point. In other words, set the Cutoff value somewhere between fully open and fully closed... set it to a value that you want to return to... that becomes the "center" that Motion Seq will return to when stopped. This can be done by shaping the CURVE. For example, the STANDARD Curve is just a steady ramp, use the Param 1 = 4 instead of the default 5. This will create a Curve the "open" the Filter early.

Option 2:
By using the [MOTION SEQ HOLD] button you can stop movement of the Motion Sequence anywhere along its movement. It accomplishes the same thing as stop, except the current controller setting is held.

The answers above are in general because you don't say if you are using the Motion Sequence Auto Knob or within a Part. If you need more specific details, let us know.

Thanks. I did this, but it doesn't help. I am trying to use the motion sequencer to modify a filter cutoff within a part. I specifically in trying to get the effect used by Emerson Lake and Palmer in carnival nine, during the welcome back my friends intro.
There must be something I'm doing incorrectly; doesn't work as you described. Should I be using an analog patch rather than digital? If you can help me anymore, thanks in advance.

Why not get some things out on the table with more clarity?

You say analog vs. digital "patches". "Patches" do come from DX7 days - so I'm guessing you're using an FM-X part as the basis of your performance (which is modulated)? If so, what's the performance or part name for the lead part?

What's the shape of your "Mod/Control" -> "Control Assign" curve. It's labeled as "Curve Type" - and what are the other parameters other than bipolar? (ratio, param1, etc).

Not knowing these, I'll setup just something representative.

1) press [PERFORMANCE] (HOME) - for sanity
2) press [CATEGORY SEARCH], then Touchscreen (TS): "Init", then touch "Init Normal (FM-X)"
3) TS: press the small font "Init Normal (FM-X)" - not the one at the top of the screen, but the one to the right of "Name" then touch "Edit"
4) TS: touch menu "Motion Seq" -> "Lane"
5) TS: Make sure part and master Motion Seq are ON, Lane 1 make sure LaneSW is ON, "Loop" should be on by default - which is what you want
Same screen - Set "Cycle" to 2 (to make it easy for the example - your cycle count depends on complexity of the sequence), Leaving key on reset OFF since I just
want the motion to trigger by the first key pressed and continue without resetting,
This menu are pulses. By default, you see the triangle and it goes from 0 to 64
NOTE: when you turn Motion Sequence "OFF" - the output of this pulse (feeding your mod control curve) is going to be the "Y" offset which is zero for uni-polar. This isn't what you want if you want a bipolar curve to stop where the curve is zero - which is typically when the pulse is equal to 64. So:
6) TS: Touch "Edit Sequence", touch "Bipolar" under "Polarity" - this fixes the "reset" condition
7) Same menu - TS: touch the box with "1" on top of green area, "64" on buttom of green area, and "A" which is below the "64". These are your pulses. Change the "Step 1 Value" to 0. Now you should see a "1" on top of the green area (for step 1), and a "0" on the bottom just above the "A"
8) TS: Change direction of Pulse A to "Reverse"
9) TS: Touch the "A" for step 2 (should say "2" above the green area, "64" below the green area just above the "A" you should touch) - This will change it to "B" for pulse 2.
10) TS: Touch the blue area for step 2 and set the "Step 2 Value" to 127
Note: this pattern may not do exactly what you want to do, but at least it runs through the entire mod control curve starting with 0 then ramping up increasing valus to 127, then cycles back to 0 again (so this jump from 127 to 0 may not be what you want). Not really part of this example.
11) TS: Touch left-hand side menu "Mod / Control" -> "Control Assign"
12) TS: Touch "Display Filter" and select "MS Lane 1" - you may have to press the expand all icon which looks like a 3x4 grid of "=" signs to see the "MS Lane 1" or scroll with the "up" and "down" arrows on the touchscreen.
13) TS: Press the [+] button to add a destination, it defaults as "InsA Param 1", touch the destination under "Destination 1" to change it. Since this is FM, you can select "FM Param" -> "Cutoff", then press the [ENTER] button
14) TS: Change polarity to "Bi", set "Ratio" to +63 for most dramatic effect
15) Note, "Cutoff" doesn't make any sense without a filter - so we have to add one to the FM-X init performance since it defaults without one.
TS: Touch left-hand menu "Pitch/Filter" -> "Filter Type" - change from "Thru" to "LPF24D" - or anything. You may need to press the 3x4 grid of "=" to see all options.

Now you're ready to hear the filter in action. Strike a chord.

The [MOTION SEQ/OFF] switch should be illuminated since we earlier set both part and master motion sequence ON. Press the button to turn the LED off (motion sequence off).

Since we've used intentional use of the pulse vs. curve reset conditions - when you turn OFF motion sequence, the pulse is set to 64 which is the mid-point where your bi-polar ramp crosses the Y-axis (is zero) and therefore will reset to "0" instead of some extreme negative or positive value (depending on the curve's ramp direction).

Also be aware that the cure output of "0" is exactly what you want. What this means is "influence on the original cutoff value". An influence of 0 means it is not changed vs. the performance's default. An influence of -60 would mean cutoff would be "rolled back" by 60 and an influence of +60 means the cutoff would be augmented (dialed up) by 60. The curve output is not the value of cutoff - it's how much is added or subtracted from the performance's set value.

Thanks for all your efforts!