I would not prefer to make a reinstall.
Indexing V2 labours us for about 1 year now. Index V1 and V2 are not comporable.
However, I can just speak for my environment and based on my experience I'd check the following
1.) Download the Index State Report, Deploy it, have a look at it - does EVERY IndexV2 Client have an IndexServer where it can connect to? Please check EACH Client!
a) If so, feel comfortable
b) If not, change every wrong set IndexServer. Do so either by klicking the defaultbackupset of the client and check the Tab "Index", or use the change Index-Server-Workflow
2.) Are there IndexRestores triggered automatically in your Environment? That should tell you, if Indexes are consistent or not. However, this can be a result of 1b) as well!
If IndexRestores are triggered, have a look for which client those are triggered and look, if you can even browse the data. Without Warranty from my side, if Indexreconstructions/Indexrestores fail, maybe you can use the Regkeys
The above comes with no warranty - it just worked in our environment.
3.) Are there Storagepolicies where per storagepolicy the Data Paths which are put into it can NOT communicate with each other?
if so: immediately disable the autoscheduler for Indexing Loadbalance
and if so: Ask Commvault for a special Workflow to use EACH DataPath while Backup up Index.
So far from my side. Maybe you can share a reply and we can have a deeper understanding together.